From 9b668c1b6e0e0b290e5fce3ff8f44cce168c3ab6 Mon Sep 17 00:00:00 2001
From: Adam Caprez <acaprez2@unl.edu>
Date: Fri, 26 Oct 2018 19:05:55 +0000
Subject: [PATCH] Initial commit of converted markdown from Confluence.
---
archetypes/default.md | 6 +
config.toml | 73 +
content/_footer.md | 5 +
content/_index.md | 120 +
content/contact_us/_index.md | 42 +
content/events/_index.md | 9 +
.../events/august_2014_uno_hcc_workshop.md | 38 +
content/events/hcc_condor_workshop_2013.md | 87 +
content/events/hcc_fall_kickstart_2015.md | 77 +
content/events/hcc_fall_kickstart_2016.md | 94 +
content/events/hcc_matlab_workshop_2013.md | 107 +
content/events/hcc_mpi_workshop_2013.md | 55 +
content/events/hcc_qiime_workshop_2016.md | 102 +
content/events/hcc_spring_workshop_uno.md | 21 +
content/events/hcc_users_group.md | 32 +
content/events/hgrlab_anvil_presentation.md | 31 +
...instructions_for_52016_allinea_workshop.md | 228 +
.../july_2014_bioinformatics_workshop.md | 35 +
content/events/june_2013_osg_workshop.md | 59 +
.../june_2014_bioinformatics_workshop.md | 62 +
content/events/june_workshop_series_2017.md | 93 +
content/events/june_workshop_series_2018.md | 32 +
.../nebraska_supercomputing_symposium_12.md | 80 +
...014_hcc_workshop_college_of_engineering.md | 36 +
...workshop_earth_and_atmospheric_sciences.md | 47 +
...ence_grid_workshop_unl_january_6_8_2016.md | 38 +
.../software_carpentry_workshop_setup.md | 108 +
...carpentry_workshop_unl_january_5_6_2017.md | 55 +
...carpentry_workshop_unl_january_8_9_2015.md | 29 +
..._carpentry_workshop_unl_july_15_16_2015.md | 35 +
...carpentry_workshop_unl_march_20_21_2015.md | 35 +
...carpentry_workshop_unl_march_27_28_2017.md | 64 +
...arpentry_workshop_unl_november_5_6_2015.md | 36 +
...carpentry_workshop_uno_april_22_23_2015.md | 35 +
..._carpentry_workshop_uno_july_14_15_2016.md | 56 +
.../supercomputing_mini_workshop_2012.md | 43 +
...omputing_mini_workshop_february_27_2013.md | 198 +
.../unk_linear_algebra_feb_28th_2017.md | 270 +
...umerical_analysis_class_august_5th_2016.md | 31 +
...unl_r_for_biologists_class_march_8_2017.md | 311 +
.../events/unl_stat802_january_23rd_2017.md | 43 +
content/events/unl_stat_802_fall_2017.md | 71 +
content/events/unl_stat_850_fall_2017.md | 42 +
content/events/unl_stat_850_fall_2018.md | 42 +
content/events/unl_stat_950_fall_2017.md | 29 +
.../unl_stat_alpha_seminar_fall_2017.md | 39 +
content/events/xsede_big_data.md | 36 +
.../xsede_workshop_big_data_november_2016.md | 42 +
.../xsede_workshop_openacc_december_2016.md | 36 +
content/faq/_index.md | 201 +
content/guides/_index.md | 9 +
content/guides/anvil/_index.md | 232 +
content/guides/anvil/adding_ssh_key_pairs.md | 84 +
content/guides/anvil/anvil_instance_types.md | 111 +
content/guides/anvil/available_images.md | 186 +
.../connecting_to_linux_instances_from_mac.md | 88 +
...necting_to_linux_instances_from_windows.md | 131 +
...onnecting_to_linux_instances_using_x2go.md | 106 +
.../anvil/connecting_to_the_anvil_vpn.md | 96 +
.../anvil/connecting_to_windows_instances.md | 167 +
content/guides/anvil/creating_an_instance.md | 100 +
.../anvil/creating_and_attaching_a_volume.md | 90 +
.../anvil/creating_ssh_key_pairs_on_mac.md | 66 +
.../creating_ssh_key_pairs_on_windows.md | 99 +
...rmatting_and_mounting_a_volume_in_linux.md | 168 +
...atting_and_mounting_a_volume_in_windows.md | 137 +
content/guides/anvil/resizing_an_instance.md | 130 +
.../what_are_the_per_group_resource_limits.md | 40 +
content/guides/handling_data/_index.md | 172 +
.../handling_data/data_for_unmc_users_only.md | 60 +
.../handling_data/globus_connect/_index.md | 181 +
.../activating_hcc_cluster_endpoints.md | 106 +
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.../file_transfers_between_endpoints.md | 68 +
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.../handling_data/preventing_file_loss.md | 172 +
content/guides/handling_data/using_attic.md | 117 +
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content/guides/running_applications/_index.md | 13 +
.../allinea_performance_reports.md | 168 +
.../allinea_profiling_debugging_tools.md | 29 +
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.../bamtools/running_bamtools_commands.md | 287 +
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.../de_novo_assembly_tools/soapdenovo2.md | 291 +
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.../running_trinity_in_multiple_steps.md | 163 +
.../de_novo_assembly_tools/velvet/_index.md | 173 +
.../running_velvet_with_paired_end_data.md | 1331 ++++
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.../running_velvet_with_single_end_data.md | 104 +
.../downloading_sra_data_from_ncbi.md | 89 +
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.../cufflinks.md | 2860 +++++++++
.../_index.md | 16 +
.../cap3.md | 160 +
.../cd_hit.md | 118 +
.../compiling_an_openmp_application.md | 56 +
.../compiling_source_code.md | 38 +
.../dmtcp_checkpointing.md | 1125 ++++
.../installing_perl_modules.md | 68 +
.../running_applications/module_commands.md | 175 +
.../running_gaussian_at_hcc.md | 274 +
...unning_ocean_land_atmosphere_model_olam.md | 1536 +++++
.../running_applications/running_theano.md | 105 +
.../using_anaconda_package_manager.md | 289 +
.../running_applications/using_singularity.md | 325 +
content/guides/submitting_jobs/_index.md | 228 +
...vailable_partitions_on_crane_and_tusker.md | 623 ++
.../available_partitions_on_sandhills.md | 109 +
.../hcc_acknowledgment_credit.md | 341 +
.../submitting_jobs/job_dependencies.md | 181 +
.../guides/submitting_jobs/monitoring_jobs.md | 148 +
.../submitting_jobs/submitting_a_job_array.md | 56 +
.../submitting_an_interactive_job.md | 70 +
.../submitting_jobs/submitting_an_mpi_job.md | 1346 ++++
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.../submitting_cuda_or_openacc_jobs.md | 1428 +++++
.../submitting_htcondor_jobs.md | 57 +
.../guides/submitting_jobs/submitting_jobs.md | 229 +
.../submitting_jobs/submitting_matlab_jobs.md | 1360 ++++
.../submitting_jobs/submitting_r_jobs.md | 1611 +++++
content/quickstarts/_index.md | 10 +
content/quickstarts/bash_commands.md | 217 +
content/quickstarts/condor_jobs_on_hcc.md | 264 +
content/quickstarts/for_maclinux_users.md | 207 +
content/quickstarts/for_windows_users.md | 153 +
content/quickstarts/fortranc_on_hcc.md | 1559 +++++
.../how_to_change_your_password.md | 132 +
.../how_to_setup_x11_forwarding.md | 102 +
content/quickstarts/mpi_jobs_on_hcc.md | 1645 +++++
...reusing_ssh_connections_in_linux_or_mac.md | 40 +
.../quickstarts/setting_up_and_using_duo.md | 212 +
.../setting_up_gitlab_on_hcc_clusters.md | 114 +
.../quickstarts/using_unl_gitlab_instance.md | 78 +
static/images/7700509.jpeg | Bin 0 -> 138486 bytes
168 files changed, 56447 insertions(+)
create mode 100644 archetypes/default.md
create mode 100644 config.toml
create mode 100644 content/_footer.md
create mode 100644 content/_index.md
create mode 100644 content/contact_us/_index.md
create mode 100644 content/events/_index.md
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create mode 100644 content/events/hcc_fall_kickstart_2015.md
create mode 100644 content/events/hcc_fall_kickstart_2016.md
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create mode 100644 content/events/hcc_spring_workshop_uno.md
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create mode 100644 content/events/hgrlab_anvil_presentation.md
create mode 100644 content/events/instructions_for_52016_allinea_workshop.md
create mode 100644 content/events/july_2014_bioinformatics_workshop.md
create mode 100644 content/events/june_2013_osg_workshop.md
create mode 100644 content/events/june_2014_bioinformatics_workshop.md
create mode 100644 content/events/june_workshop_series_2017.md
create mode 100644 content/events/june_workshop_series_2018.md
create mode 100644 content/events/nebraska_supercomputing_symposium_12.md
create mode 100644 content/events/october_2014_hcc_workshop_college_of_engineering.md
create mode 100644 content/events/september_2014_hcc_workshop_earth_and_atmospheric_sciences.md
create mode 100644 content/events/software_carpentry_open_science_grid_workshop_unl_january_6_8_2016.md
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create mode 100644 content/events/software_carpentry_workshop_unl_january_5_6_2017.md
create mode 100644 content/events/software_carpentry_workshop_unl_january_8_9_2015.md
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create mode 100644 content/events/supercomputing_mini_workshop_february_27_2013.md
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create mode 100644 content/events/unl_numerical_analysis_class_august_5th_2016.md
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create mode 100644 content/events/unl_stat802_january_23rd_2017.md
create mode 100644 content/events/unl_stat_802_fall_2017.md
create mode 100644 content/events/unl_stat_850_fall_2017.md
create mode 100644 content/events/unl_stat_850_fall_2018.md
create mode 100644 content/events/unl_stat_950_fall_2017.md
create mode 100644 content/events/unl_stat_alpha_seminar_fall_2017.md
create mode 100644 content/events/xsede_big_data.md
create mode 100644 content/events/xsede_workshop_big_data_november_2016.md
create mode 100644 content/events/xsede_workshop_openacc_december_2016.md
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create mode 100644 content/guides/anvil/_index.md
create mode 100644 content/guides/anvil/adding_ssh_key_pairs.md
create mode 100644 content/guides/anvil/anvil_instance_types.md
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create mode 100644 content/guides/running_applications/bioinformatics_tools/de_novo_assembly_tools/_index.md
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create mode 100644 content/quickstarts/setting_up_gitlab_on_hcc_clusters.md
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create mode 100644 static/images/7700509.jpeg
diff --git a/archetypes/default.md b/archetypes/default.md
new file mode 100644
index 00000000..00e77bd7
--- /dev/null
+++ b/archetypes/default.md
@@ -0,0 +1,6 @@
+---
+title: "{{ replace .Name "-" " " | title }}"
+date: {{ .Date }}
+draft: true
+---
+
diff --git a/config.toml b/config.toml
new file mode 100644
index 00000000..e23cb099
--- /dev/null
+++ b/config.toml
@@ -0,0 +1,73 @@
+#baseURL = "http://hcc-docs.unl.edu/"
+languageCode = "en-us"
+title = "HCC-DOCS"
+theme = "docdock"
+contentdir = "content"
+layoutdir = "layouts"
+publishdir = "public"
+baseURL = "/"
+
+DefaultContentLanguage = "en"
+pygmentsCodeFences = true
+pygmentsStyle = "monokailight"
+
+defaultContentLanguage = "en"
+defaultContentLanguageInSubdir= false
+enableMissingTranslationPlaceholders = false
+
+
+[blackfriday]
+hrefTargetBlank = true
+
+# [Languages]
+# [Languages.en]
+# title = "Documentation for Hugo docDock"
+# weight = 1
+# languageName = "English"
+#
+# [Languages.fr]
+# title = "Documentation du thème docDock"
+# weight = 2
+# languageName = "Français"
+
+
+
+
+[params]
+#editURL = "https://github.com/vjeantet/hugo-theme-docdock/edit/master/exampleSite/content/"
+showVisitedLinks = true # default is false
+themeStyle = "flex" # "original" or "flex" # default "flex"
+themeVariant = "" # choose theme variant "green", "gold" , "gray", "blue" (default)
+ordersectionsby = "weight" # ordersectionsby = "title"
+disableHomeIcon = false # default is false
+disableSearch = false # default is false
+disableNavChevron = false # set true to hide next/prev chevron, default is false
+highlightClientSide = false # set true to use highlight.pack.js instead of the default hugo chroma highlighter
+menushortcutsnewtab = false # set true to open shortcuts links to a new tab/window
+enableGitInfo = false
+
+[outputs]
+home = [ "HTML", "RSS", "JSON"]
+
+
+[[menu.shortcuts]]
+name = "HCC homepage"
+identifier = "ds"
+url = "https://hcc.unl.edu"
+weight = 10
+
+#[[menu.shortcuts]]
+#name = "<i class='fa fa-cloud-download'></i> <label>Download</label>"
+#url = "https://github.com/vjeantet/hugo-theme-docdock/archive/master.zip"
+#weight = 11
+
+#[[menu.shortcuts]]
+#name = "<i class='fa fa-bookmark'></i> <label>Hugo Documentation</label>"
+#identifier = "hugodoc"
+#url = "https://gohugo.io/"
+#weight = 20
+
+#[[menu.shortcuts]]
+#name = "<i class='fa fa-bullhorn'></i> <label>Credits</label>"
+#url = "/credits"
+#weight = 30
diff --git a/content/_footer.md b/content/_footer.md
new file mode 100644
index 00000000..12fd2f9e
--- /dev/null
+++ b/content/_footer.md
@@ -0,0 +1,5 @@
++++
+ title = "Footer"
++++
+
+{{< icon name="copyright-mark" >}} [Holland Computing Center] (https://hcc.unl.edu) | 118 Schorr Center, Lincoln NE 68588 | {{< icon name="envelope" >}}[hcc-support@unl.edu] (mailto:hcc-support@unl.edu) | {{< icon name="phone-alt" >}}402-472-5041
diff --git a/content/_index.md b/content/_index.md
new file mode 100644
index 00000000..4d3769b3
--- /dev/null
+++ b/content/_index.md
@@ -0,0 +1,120 @@
+HCC Documentation
+============================
+
+
+The Holland Computing Center supports a diverse collection of research
+computing hardware. Anyone in the University of Nebraska system is
+welcome to apply for an account on HCC machines.
+
+Access to these resources is by default shared with the rest of the user
+community via various job schedulers. These policies may be found on the
+pages for the various resources. Alternatively, a user may buy into an
+existing resource, acquiring 'priority access'. Finally, several
+machines are available via Condor for opportunistic use. This will allow
+users almost immediate access, but the job is subject to preemption.
+
+#### <a href="http://hcc.unl.edu/new-user-request" class="external-link">New Users Sign Up</a>
+
+#### [Quick Start Guides](/quickstarts)
+
+Which Cluster to Use?
+---------------------
+
+**Crane**: Crane is the newest and most powerful HCC resource . If you
+are new to using HCC resources, Crane is the recommended cluster to use
+initially. Limitations: Crane has only 2 CPU/16 cores and 64GB RAM per
+node. If your job requires more than 16 cores per node or you need more
+than 64GB of memory, consider using Tusker instead.
+
+**Tusker**: Similar to Crane, Tusker is another cluster shared by all
+campus users. It has 4 CPU/ 64 cores and 256GB RAM per nodes. Two nodes
+have 512GB RAM for very large memory jobs. So for jobs requiring more
+than 16 cores per node or large memory, Tusker would be a better option.
+
+**Sandhills**: Sandhills is a condominium-style cluster, and the
+majority is owned by various research groups on campus. Jobs from
+resource owners have first priority in their owned partitions. Users
+that do not own resources (Guests) can do opportunistic computation, but
+we would recommend using Crane or Tusker.
+
+User Login
+----------
+
+For Windows users, please refer to this link [For Windows
+Users](https://hcc-docs.unl.edu/display/HCCDOC/For+Windows+Users). For
+Mac or Linux users, please refer to this link [For Mac/Linux
+Users](https://hcc-docs.unl.edu/pages/viewpage.action?pageId=2851290).
+
+**Logging into Crane or Tusker**
+
+{{< highlight bash >}}
+ssh crane.unl.edu -l <username>
+or
+ssh tusker.unl.edu -l <username>
+or
+ssh sandhills.unl.edu -l <username>
+{{< /highlight >}}
+
+Duo Security
+------------
+
+Duo two-factor authentication is **required** for access to HCC
+resources. Registration and usage of Duo security can be found in this
+section: [Setting up and using
+Duo](https://hcc-docs.unl.edu/display/HCCDOC/Setting+up+and+using+Duo)
+
+**Important Notes**
+
+- The Crane, Tusker and Sandhills clusters are separate. But, they are
+ similar enough that submission scripts on whichever one will work on
+ another, and vice versa.
+
+- The worker nodes cannot write to the `/home` directories. You must
+ use your `/work` directory for processing in your job. You may
+ access your work directory by using the command:
+{{< highlight bash >}}
+$ cd $WORK
+{{< /highlight >}}
+
+Resources
+---------
+
+- <span style="color: rgb(0,0,0);">Crane</span> - HCC's newest
+ machine, Crane has 7232 Intel Xeon cores in 452 nodes with 64GB RAM
+ per node.
+
+- Tusker - consists of 106 AMD Interlagos-based nodes (6784 cores)
+ interconnected with Mellanox QDR Infiniband.
+
+- Sandhills - has 1440 AMD cores housed in 42 nodes with 128GB per
+ node and 2 nodes with 256GB per node.
+
+- <a href="http://hcc.unl.edu/red/index.php" class="external-link">Red </a>-
+ This cluster is the resource for UNL's US CMS Tier-2 site.
+
+ - <a href="http://www.uscms.org/" class="external-link">CMS</a>
+ - <a href="http://www.opensciencegrid.org/" class="external-link">Open Science Grid</a>
+ - <a href="https://myosg.grid.iu.edu/" class="external-link">MyOSG</a>
+
+- [Glidein](The-Open-Science-Grid_11635314.html) - A gateway to
+ running jobs on the OSG, a collection of computing resources across
+ the US.
+- Anvil - HCC's cloud computing cluster based on Openstack
+
+Resource Capabilities
+---------------------
+
+| Cluster | Overview | Processors | RAM | Connection | Storage
+| ------- | ---------| ---------- | --- | ---------- | ------
+| **Crane** | 548 node Production-mode LINUX cluster | 452 Intel Xeon E5-2670 2.60GHz 2 CPU/16 cores per node<br> <br>116 Intel Xeon E5-2697 v4 2.3GHz, 2 CPU/36 cores per node<br><br>("CraneOPA") | 452 nodes @ \*64GB<br><br>79 nodes @ \*\*256GB<br><br>37 nodes @ \*\*\*512GB | QDR Infiniband<br><br>EDR Omni-Path Architecture | ~1.8 TB local scratch per node<br><br>~4 TB local scratch per node<br><br>~1452 TB shared Lustre storage
+| **Tusker** | 82 node Production-mode LINUX cluster | Opteron 6272 2.1GHz, 4 CPU/64 cores per node | \*\*256 GB RAM per node<br>\*\*\*2 Nodes with 512GB per node<br>\*\*\*\*1 Node with 1024GB per node | QDR Infiniband | ~500 TB shared Lustre storage<br>~500GB local scratch |
+| **Sandhills** | 108 node Production-mode LINUX cluster (condominium model) | 62 4-socket Opteron 6376 (2.3 Ghz, 64 cores/node)<br>44 4-socket Opteron 6128 (2.0 Ghz, 32 cores/node)<br>2 4-socket Opteron 6168 (1.9 Ghz, 48 cores/node) | 62 nodes @ 192GB<br>44 nodes @ 128GB<br>2 nodes @ 256GB | QDR Infiniband<br>Gigabit Ethernet | 175 TB shared Lustre storage<br>~1.5TB per node
+| **Red** | 344 node Production-mode LINUX cluster | Various Xeon and Opteron processors 7,280 cores maximum, actual number of job slots depends on RAM usage | 1.5-4GB RAM per job slot | 1Gb, 10Gb, and 40Gb Ethernet | ~6.67PB of raw storage space |
+| **Anvil** | 76 Compute nodes (Partially used for cloud, the rest used for general computing), 12 Storage nodes, 2 Network nodes Openstack cloud | 76 Intel Xeon E5-2650 v3 2.30GHz 2 CPU/20 cores per node | 76 nodes @ 256GB | 10Gb Ethernet | 528 TB Ceph shared storage (349TB available now) |
+
+You may only request the following amount of RAM: <br>
+\*62.5GB <br>
+\*\*250GB <br>
+\*\*\*500GB <br>
+\*\*\*\*1000GB
+
diff --git a/content/contact_us/_index.md b/content/contact_us/_index.md
new file mode 100644
index 00000000..2b84f6e5
--- /dev/null
+++ b/content/contact_us/_index.md
@@ -0,0 +1,42 @@
++++
+title = "Contact Us"
+weight = "90"
++++
+
+<span id="title-text"> HCC-DOCS : Contact Us </span>
+====================================================
+
+Created by <span class="author"> John Thiltges</span>, last modified by
+<span class="editor"> Carrie Brown</span> on Jun 25, 2018
+
+If you have questions, please contact us at
+<a href="mailto:hcc-support@unl.edu" class="external-link">hcc-support@unl.edu</a>,
+or stop by one of our locations.
+
+**Lincoln**
+
+118 SHOR
+1100 T St
+Lincoln, NE 68588-0150
+
+<a href="https://maps.google.com/maps?q=Schorr+Center%E2%80%8E+University+of+Nebraska-Lincoln,+Lincoln,+NE+68508" class="external-link">Map</a>
+
+**Omaha**
+
+152 PKI
+<span class="pp-headline-item pp-headline-address"> 1110 S 67th
+St</span>
+Omaha, NE 68106
+
+<a href="https://maps.google.com/maps?cid=15059268209840552421" class="external-link">Map</a>
+
+
+
+Or contact one of
+us <a href="https://hcc.unl.edu/contact-us" class="external-link">directly.</a>
+
+
+
+Document generated by Confluence on Oct 24, 2018 14:56
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/events/_index.md b/content/events/_index.md
new file mode 100644
index 00000000..ebe642f4
--- /dev/null
+++ b/content/events/_index.md
@@ -0,0 +1,9 @@
++++
+title = "Events"
+weight = "30"
++++
+
+HCC Events
+----------
+
+{{% children %}}
diff --git a/content/events/august_2014_uno_hcc_workshop.md b/content/events/august_2014_uno_hcc_workshop.md
new file mode 100644
index 00000000..2ba54af7
--- /dev/null
+++ b/content/events/august_2014_uno_hcc_workshop.md
@@ -0,0 +1,38 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [HCC Events](HCC-Events_332364.html)
+
+<span id="title-text"> HCC-DOCS : August 2014 UNO HCC Workshop </span>
+======================================================================
+
+Created by <span class="author"> Emelie Harstad</span>, last modified on
+Aug 29, 2014
+
+When: August 29, 2014
+
+Where: UNO Criss Library room 232
+
+<a href="http://hcc.unl.edu/fall-workshop-august-29-uno" class="external-link">Registration</a>
+
+Please bring a laptop.
+
+Download Slides: [ppt](attachments/8192949/8127063.pptx)
+[ ](attachments/8192949/8127064.pdf)[PDF](attachments/8192949/8127064.pdf)
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[HCC\_UNO\_Workshop\_Aug\_2014.pptx](attachments/8192949/8127063.pptx)
+(application/vnd.openxmlformats-officedocument.presentationml.presentation)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[HCC\_UNO\_Workshop\_Aug\_2014.pdf](attachments/8192949/8127065.pdf)
+(application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[HCC\_UNO\_Workshop\_Aug\_2014.pdf](attachments/8192949/8127064.pdf)
+(application/pdf)
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/events/hcc_condor_workshop_2013.md b/content/events/hcc_condor_workshop_2013.md
new file mode 100644
index 00000000..67427f76
--- /dev/null
+++ b/content/events/hcc_condor_workshop_2013.md
@@ -0,0 +1,87 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [HCC Events](HCC-Events_332364.html)
+
+<span id="title-text"> HCC-DOCS : HCC Condor Workshop 2013 </span>
+==================================================================
+
+Created by <span class="author"> Huang Cheng-Wei</span>, last modified
+on Jun 25, 2013
+
+Quick
+link: <a href="http://go.unl.edu/hcc_condor_2013" class="external-link">http://go.unl.edu/hcc_condor_2013</a>
+
+<span
+class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
+class="expand-control-text">Click here to view presentation...</span>
+
+Presentation
+============
+
+Workshop presentation slides
+<[condor\_workshop.pdf](attachments/2851573/3178564.pdf)>
+
+| Time | Title | Description |
+|---------|-------------------------|------------------------------------------------|
+| 1pm-2pm | Demo/Hand-On Practice | Executing Condor jobs on HCC supertcomputers |
+| 2pm-3pm | Individual Consultation | Bring your research code on HCC supercomputers |
+
+Password for all demo accounts is **HCC\_condor2013**.
+Replace `<group name>` with `demo` and `<username>` with `demoXX` (e.g. `demo01`).
+
+- Get started with [For Windows
+ Users](For-Windows-Users_2851288.html) or [For Mac/Linux
+ Users](2851290.html).
+- Sample code for Fortran/C on HCC:
+ <[serial\_dir.zip](attachments/2851569/3178562.zip)>
+- Sample code for Condor on HCC:
+ <[condor\_dir.zip](attachments/2851573/3178565.zip)>
+- For more details of this demonstration, see [Condor Jobs on
+ HCC](Condor-Jobs-on-HCC_2851447.html).
+
+
+
+<span
+class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
+class="expand-control-text">Click here to view presentation...</span>
+
+Error rendering macro 'viewpdf' : The viewfile macro is unable to locate
+the attachment "matlab\_workshop.pdf" on this page
+
+Presentation
+============
+
+Workshop presentation slides
+<[matlab\_workshop.pdf](attachments/2851357/3178542.pdf)>
+
+| Time | Title | Description |
+|---------|-------------------------|---------------------------------------------------|
+| 1pm-2pm | Demo/Hand-On Practice | Implementing a MATLAB code on HCC supertcomputers |
+| 2pm-3pm | Individual Consultation | Bring your MATLAB code on HCC supercomputers |
+
+Password for all demo accounts is **HCC\_matlab2013**.
+Replace `<group name>` with `demo` and `<username>` with `demoXX` (e.g. `demo01`).
+
+- Get started with [For Windows
+ Users](For-Windows-Users_2851288.html) or [For Mac/Linux
+ Users](2851290.html).
+- Sample code for MATLAB on HCC:
+ <[matlab\_dir.zip](attachments/2851357/3178543.zip)>
+- Sample code for Parallel MATLAB Job:
+ <[parallel\_matlab\_dir.zip](attachments/2851357/3178544.zip)>
+- For more details of this demonstration, see [MATLAB on
+ HCC](MATLAB-on-HCC_2851078.html).
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[condor\_workshop.pdf](attachments/2851573/3178564.pdf)
+(application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[condor\_dir.zip](attachments/2851573/3178565.zip) (application/zip)
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/events/hcc_fall_kickstart_2015.md b/content/events/hcc_fall_kickstart_2015.md
new file mode 100644
index 00000000..7f7bd165
--- /dev/null
+++ b/content/events/hcc_fall_kickstart_2015.md
@@ -0,0 +1,77 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [HCC Events](HCC-Events_332364.html)
+
+<span id="title-text"> HCC-DOCS : HCC Fall KickStart - 2015 </span>
+===================================================================
+
+Created by <span class="author"> Emelie Harstad</span>, last modified on
+Sep 08, 2015
+
+When: September 8-9, 2015
+
+Where: UNL City Campus Nebraska Union - Colonial Room
+
+Quick
+Link: <a href="http://go.unl.edu/kickstart2015" class="external-link">http://go.unl.edu/kickstart2015</a>
+
+------------------------------------------------------------------------
+
+Materials
+---------
+
+Etherpad: <a href="https://etherpad.mozilla.org/2015-09-08" class="external-link">https://etherpad.mozilla.org/2015-09-08</a>
+
+Software Carpentry
+Lessons: <a href="http://eharstad.github.io/2015-09-08-UNL/" class="external-link">http://eharstad.github.io/2015-09-08-UNL/</a>
+
+Slides for Day 1 (Software Carpentry Introduction):
+
+ <span
+class="confluence-embedded-file-wrapper"><a href="/download/attachments/11636707/Kickstart-UNL-20150908.pptx?version=1&modificationDate=1441398235000&api=v2" class="confluence-embedded-file"><img src="assets/images/documentConversion/latest/conversion/thumbnail/11636708/1" height="250" /></a></span>
+
+Slides for Day 2 (Morning Session):
+
+[<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/11636707/11636717.png" class="confluence-embedded-image" width="335" /></span>](attachments/11636707/11636716.pdf)
+
+Slides for HCC Introduction (David):
+
+<span
+class="confluence-embedded-file-wrapper"><a href="/download/attachments/11636707/HCCintro.pdf?version=1&modificationDate=1441722144000&api=v2" class="confluence-embedded-file"><img src="assets/images/documentConversion/latest/conversion/thumbnail/11636722/1" height="250" /></a></span>
+
+
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[Kickstart-UNL-20150908.pptx](attachments/11636707/11636708.pptx)
+(application/vnd.openxmlformats-officedocument.presentationml.presentation)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[2015\_HCC\_KickStart.pdf](attachments/11636707/11636750.pdf)
+(application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[Capture.PNG](attachments/11636707/11636717.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[HCCintro.pdf](attachments/11636707/11636722.pdf) (application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[2015\_HCC\_KickStart.pdf](attachments/11636707/11636819.pdf)
+(application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[2015\_HCC\_KickStart.pdf](attachments/11636707/11636820.pdf)
+(application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[2015\_HCC\_KickStart.pdf](attachments/11636707/11636821.pdf)
+(application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[2015\_HCC\_KickStart.pdf](attachments/11636707/11636824.pdf)
+(application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[2015\_HCC\_KickStart.pdf](attachments/11636707/11636716.pdf)
+(application/pdf)
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/events/hcc_fall_kickstart_2016.md b/content/events/hcc_fall_kickstart_2016.md
new file mode 100644
index 00000000..f55f5da0
--- /dev/null
+++ b/content/events/hcc_fall_kickstart_2016.md
@@ -0,0 +1,94 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [HCC Events](HCC-Events_332364.html)
+
+<span id="title-text"> HCC-DOCS : HCC Fall KickStart - 2016 </span>
+===================================================================
+
+Created by <span class="author"> Emelie Harstad</span>, last modified by
+<span class="editor"> Adam Caprez</span> on Sep 19, 2016
+
+When: September 8-9, 2016
+
+Where: Sept. 8th - UNL City Campus Nebraska Union - Colonial Room A&B
+
+ Sept. 9th - Whittier Hall room 152
+
+Quick
+Link: <a href="http://go.unl.edu/kickstart2016" class="external-link">http://go.unl.edu/kickstart2016</a><a href="http://go.unl.edu/kickstart2015" class="external-link"></a>
+
+------------------------------------------------------------------------
+
+Materials
+---------
+
+Etherpad: <a href="https://public.etherpad-mozilla.org/p/2016-09-08-UNL" class="external-link">https://public.etherpad-mozilla.org/p/2016-09-08-UNL</a><a href="https://etherpad.mozilla.org/2015-09-08" class="external-link"></a>
+
+Software Carpentry
+Lessons: <a href="https://eharstad.github.io/2016-09-08-UNL/" class="external-link">https://eharstad.github.io/2016-09-08-UNL/</a>
+
+Slides for Thursday intro:
+
+[Kickstart-UNL-20160908.pdf](attachments/16519552/16519722.pdf)
+
+[Kickstart-UNL-20160908.pptx](attachments/16519552/16519721.pptx)
+
+
+
+Slides for Friday morning session:
+
+[HCC\_introduction.pdf](attachments/16519552/16519738.pdf)
+
+Slides for Friday afternoon session:
+
+[MPI\_overview.pdf](attachments/16519552/16519727.pdf)
+
+[MPI\_overview.ppt](attachments/16519552/16519728.ppt)
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[Kickstart-UNL-20160908.pptx](attachments/16519552/16519735.pptx)
+(application/vnd.openxmlformats-officedocument.presentationml.presentation)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[Kickstart-UNL-20160908.pdf](attachments/16519552/16519724.pdf)
+(application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[Kickstart-UNL-20160908.pdf](attachments/16519552/16519734.pdf)
+(application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[MPI\_overview.pdf](attachments/16519552/16519727.pdf)
+(application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[MPI\_overview.ppt](attachments/16519552/16519728.ppt)
+(application/vnd.ms-powerpoint)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[Kickstart-UNL-20160908.pdf](attachments/16519552/16519722.pdf)
+(application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[Kickstart-UNL-20160908.pptx](attachments/16519552/16519721.pptx)
+(application/vnd.openxmlformats-officedocument.presentationml.presentation)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[2016\_HCC\_Kickstart.pdf](attachments/16519552/16519881.pdf)
+(application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[2016\_HCC\_Kickstart.pdf](attachments/16519552/16519882.pdf)
+(application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[2016\_HCC\_Kickstart.pdf](attachments/16519552/16519884.pdf)
+(application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[2016\_HCC\_Kickstart.pdf](attachments/16519552/16519738.pdf)
+(application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[anyconnect-macosx-4.2.00096-web-deploy-k9.dmg](attachments/16519552/16519885.dmg)
+(application/x-diskcopy)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[anyconnect-win-4.2.01022-web-deploy-k9.exe](attachments/16519552/16519886.exe)
+(application/octet-stream)
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/events/hcc_matlab_workshop_2013.md b/content/events/hcc_matlab_workshop_2013.md
new file mode 100644
index 00000000..7a98af95
--- /dev/null
+++ b/content/events/hcc_matlab_workshop_2013.md
@@ -0,0 +1,107 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [HCC Events](HCC-Events_332364.html)
+
+<span id="title-text"> HCC-DOCS : HCC MATLAB Workshop 2013 </span>
+==================================================================
+
+Created by <span class="author"> Huang Cheng-Wei</span>, last modified
+by <span class="editor"> Derek Weitzel</span> on Aug 02, 2013
+
+Quick link:
+<a href="http://go.unl.edu/hcc_matlab_2013" class="external-link">http://go.unl.edu/hcc_matlab_2013</a>
+
+<span
+class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
+class="expand-control-text">Click here to view presentation...</span>
+
+Timeline
+========
+
+Workshop presentation slides
+<[matlab\_workshop.pdf](attachments/2851357/3178542.pdf)>
+
+Time
+
+Title
+
+Description
+
+UNMC
+
+10am - 11am
+
+Demo/Hand-On Practice
+
+Implementing a MATLAB code on HCC supercomputers
+
+11am - 12pm
+
+Individual Consultation
+
+Bring your MATLAB code on HCC supercomputers
+
+UNO
+
+2pm - 3pm
+
+Demo/Hand-On Practice
+
+Implementing a MATLAB code on HCC supercomputers
+
+3pm - 4pm
+
+Individual Consultation
+
+Bring your MATLAB code on HCC supercomputers
+
+
+
+Password for all demo accounts is **HCC\_matlab2013**.
+Replace `<group name>` with `demo` and `<username>` with `demoXX`
+(e.g. `demo01`).
+
+- Get started with [For Windows Users](For-Windows-Users_2851288.html)
+ or [For Mac/Linux Users](2851290.html).
+- Hands On: [MATLAB on HCC](MATLAB-on-HCC_2851078.html)
+- Sample code for MATLAB on HCC:
+ <[matlab\_dir.zip](attachments/2851357/3178543.zip)>
+- Sample code for Parallel MATLAB Job:
+ <[parallel\_matlab\_dir.zip](attachments/2851357/3178544.zip)>
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[demo\_hcc\_matlab.zip](attachments/2851357/3178541.zip)
+(application/zip)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[matlab\_workshop.pdf](attachments/2851357/3178545.pdf)
+(application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[matlab\_dir.zip](attachments/2851357/3178569.zip) (application/zip)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[parallel\_matlab\_dir.zip](attachments/2851357/3178570.zip)
+(application/zip)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[matlab\_workshop.pdf](attachments/2851357/3178546.pdf)
+(application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[matlab\_workshop.pdf](attachments/2851357/3178547.pdf)
+(application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[matlab\_workshop.pdf](attachments/2851357/3178568.pdf)
+(application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[matlab\_workshop.pdf](attachments/2851357/3178542.pdf)
+(application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[matlab\_dir.zip](attachments/2851357/3178543.zip) (application/zip)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[parallel\_matlab\_dir.zip](attachments/2851357/3178544.zip)
+(application/zip)
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/events/hcc_mpi_workshop_2013.md b/content/events/hcc_mpi_workshop_2013.md
new file mode 100644
index 00000000..a761509d
--- /dev/null
+++ b/content/events/hcc_mpi_workshop_2013.md
@@ -0,0 +1,55 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [HCC Events](HCC-Events_332364.html)
+
+<span id="title-text"> HCC-DOCS : HCC MPI Workshop 2013 </span>
+===============================================================
+
+Created by <span class="author"> Huang Cheng-Wei</span>, last modified
+on Jun 25, 2013
+
+Quick
+link: <a href="http://go.unl.edu/hcc_mpi_2013" class="external-link">http://go.unl.edu/hcc_mpi_2013</a>
+
+<span
+class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
+class="expand-control-text">Click here to view presentation...</span>
+
+Presentation
+============
+
+Workshop presentation slides
+<[mpi\_workshop.pdf](attachments/2851569/3178561.pdf)>
+
+| Time | Title | Description |
+|---------|-------------------------|------------------------------------------------|
+| 1pm-2pm | Demo/Hand-On Practice | Implementing a MPI code on HCC supertcomputers |
+| 2pm-3pm | Individual Consultation | Bring your research code on HCC supercomputers |
+
+Password for all demo accounts is **HCC\_mpi2013**.
+Replace `<group name>` with `demo` and `<username>` with `demoXX` (e.g. `demo01`).
+
+- Get started with [For Windows
+ Users](For-Windows-Users_2851288.html) or [For Mac/Linux
+ Users](2851290.html).
+- Sample code for Fortran/C on HCC:
+ <[serial\_dir.zip](attachments/2851569/3178562.zip)>
+- Sample code for MPI on HCC:
+ <[mpi\_dir.zip](attachments/2851569/3178563.zip)>
+- For more details of this demonstration, see [MPI Jobs on
+ HCC](MPI-Jobs-on-HCC_2851393.html).
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[mpi\_workshop.pdf](attachments/2851569/3178561.pdf) (application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[serial\_dir.zip](attachments/2851569/3178562.zip) (application/zip)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[mpi\_dir.zip](attachments/2851569/3178563.zip) (application/zip)
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/events/hcc_qiime_workshop_2016.md b/content/events/hcc_qiime_workshop_2016.md
new file mode 100644
index 00000000..6bdec782
--- /dev/null
+++ b/content/events/hcc_qiime_workshop_2016.md
@@ -0,0 +1,102 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [HCC Events](HCC-Events_332364.html)
+
+<span id="title-text"> HCC-DOCS : HCC QIIME Workshop - 2016 </span>
+===================================================================
+
+Created by <span class="author"> Emelie Harstad</span>, last modified on
+Oct 21, 2016
+
+When: October 20, 2016
+
+Where: NIC Food Innovation Campus room 277
+
+ 1901 N. 21st St., Lincoln, 68588
+
+Quick
+Link: <a href="http://go.unl.edu/hccqiime2016" class="external-link">http://go.unl.edu/hccqiime2016</a>
+
+<a href="https://hcc.unl.edu/hcc-qiime-workshop" class="external-link">Details and Agenda</a>
+
+<a href="https://marketplace.unl.edu/default/hcc-qiime-workshop.html" class="external-link">Registration Page</a>
+
+------------------------------------------------------------------------
+
+Materials
+---------
+
+Slides for morning
+introduction: [QIIME\_2016\_intro.pdf](attachments/16520950/16521053.pdf)
+
+Software Carpentry Unix Shell
+Lessons: <a href="http://eharstad.github.io/shell-novice/" class="external-link">http://eharstad.github.io/shell-novice/</a>
+
+Slides for HCC
+Overview: [2016\_Qiime.pdf](attachments/16520950/16521050.pdf)
+
+QIIME
+slides: [QIIME\_Talk\_Oct20.pdf](attachments/16520950/16521073.pdf)
+
+QIIME
+tutorial: <a href="http://bioinformatics.unl.edu/qiime_tutorial.pdf" class="external-link">http://bioinformatics.unl.edu/qiime_tutorial.pdf</a><a href="http://bioinformatics.unl.edu/qiime_tutorial.pdf" class="external-link"></a>
+
+------------------------------------------------------------------------
+
+**What you need to do before Thursday October 20th**
+----------------------------------------------------
+
+*Participants will need to bring a laptop with them to the workshop.* In addition, there are a few things that are required to be completed before you arrive:
+--------------------------------------------------------------------------------------------------------------------------------------------------------------
+
+1. To participate in this workshop, you will need to
+ <a href="http://hcc.unl.edu/new-user-request" class="external-link">sign up for an HCC account</a>
+ (if you do not already have one). Please complete the account
+ application and [DUO two-factor authentication
+ setup](https://hcc-docs.unl.edu/display/HCCDOC/Setting+up+and+using+Duo)
+ before Thursday. This process requires advisor approval (via email)
+ and a visit to the HCC offices in the Schorr Center to activate your
+ account, so it can sometimes take a day or more to complete. Please
+ plan accordingly. If you still do not have your account set up by
+ Thursday, please arrive at the workshop by 8:30AM to get help.
+2. Once you have your HCC account and DUO set up, please make sure that
+ you are able to log into the HCC clusters (instructions for [Windows
+ Users](https://hcc-docs.unl.edu/display/HCCDOC/For+Windows+Users)
+ and [Mac/Linux
+ Users](https://hcc-docs.unl.edu/pages/viewpage.action?pageId=2851290)).
+ If you have any problems logging in, please email us at
+ <a href="mailto:hcc-support@unl.edu" class="external-link">hcc-support@unl.edu</a>.
+3. On Thursday we will be demonstrating how to transfer files using
+ Globus Connect. Before arriving at the workshop, please log in to
+ the
+ <a href="https://www.globus.org/app/transfer" class="external-link">Globus Web App</a>
+ using your My.UNL credentials (choose *University of
+ Nebraska-Lincoln* from the drop down menu). Next, install the
+ Globus Connect Personal app on your laptop (directions for
+ <a href="https://docs.globus.org/how-to/globus-connect-personal-mac/" class="external-link">Mac OS X</a>,
+ <a href="https://docs.globus.org/how-to/globus-connect-personal-linux/" class="external-link">Linux</a>,
+ and
+ <a href="https://docs.globus.org/how-to/globus-connect-personal-windows/" class="external-link">Windows</a>)
+ so that you can begin using Globus to transfer data to and from your
+ laptop.
+
+
+
+
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[2016\_Qiime.pdf](attachments/16520950/16521050.pdf) (application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[QIIME\_2016\_intro.pdf](attachments/16520950/16521053.pdf)
+(application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[QIIME\_Talk\_Oct20.pdf](attachments/16520950/16521073.pdf)
+(application/pdf)
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/events/hcc_spring_workshop_uno.md b/content/events/hcc_spring_workshop_uno.md
new file mode 100644
index 00000000..6664784a
--- /dev/null
+++ b/content/events/hcc_spring_workshop_uno.md
@@ -0,0 +1,21 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [HCC Events](HCC-Events_332364.html)
+
+<span id="title-text"> HCC-DOCS : HCC Spring Workshop UNO </span>
+=================================================================
+
+Created by <span class="author"> Jingchao Zhang</span> on Mar 10, 2016
+
+**When**: 12:30 pm - 15:00 pm, March 11, 2016
+
+**Where**: <span style="color: rgb(91,91,90);">UNO, Criss Library Room
+249</span>
+
+**Quick
+Link**: <a href="http://jingchaozhang.github.io/2016-03-11-UNO/" class="external-link">http://jingchaozhang.github.io/2016-03-11-UNO/</a>
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/events/hcc_users_group.md b/content/events/hcc_users_group.md
new file mode 100644
index 00000000..62858bc8
--- /dev/null
+++ b/content/events/hcc_users_group.md
@@ -0,0 +1,32 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [HCC Events](HCC-Events_332364.html)
+
+<span id="title-text"> HCC-DOCS : HCC Users Group </span>
+=========================================================
+
+Created by <span class="author"> Carrie Brown</span> on Mar 17, 2017
+
+Next Meeting: TBA - Add your email address to the sign in sheet to be notified
+------------------------------------------------------------------------------
+
+March 17th 2017: HCCGo by Derek Weitzel
+---------------------------------------
+
+### Avery 108 3 to 4 pm
+
+[Speaker Slides](attachments/17043472/17043471.pdf)
+
+
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[HCCGo-3-17-17.pdf](attachments/17043472/17043471.pdf)
+(application/pdf)
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/events/hgrlab_anvil_presentation.md b/content/events/hgrlab_anvil_presentation.md
new file mode 100644
index 00000000..f3a1fada
--- /dev/null
+++ b/content/events/hgrlab_anvil_presentation.md
@@ -0,0 +1,31 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [HCC Events](HCC-Events_332364.html)
+
+<span id="title-text"> HCC-DOCS : HGRLab Anvil Presentation </span>
+===================================================================
+
+Created by <span class="author"> Natasha Pavlovikj</span>, last modified
+on Jul 31, 2017
+
+Meeting: 07/25/2017
+
+Time: 3pm
+
+Presentation
+slides: [hgrlab\_anvil.pdf](attachments/21070371/21070533.pdf)
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hgrlab\_anvil.pdf](attachments/21070371/21070373.pdf)
+(application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hgrlab\_anvil.pdf](attachments/21070371/21070533.pdf)
+(application/pdf)
+
+Document generated by Confluence on Oct 24, 2018 14:56
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/events/instructions_for_52016_allinea_workshop.md b/content/events/instructions_for_52016_allinea_workshop.md
new file mode 100644
index 00000000..a3e4c3f5
--- /dev/null
+++ b/content/events/instructions_for_52016_allinea_workshop.md
@@ -0,0 +1,228 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [HCC Events](HCC-Events_332364.html)
+
+<span id="title-text"> HCC-DOCS : Instructions for 5/20/16 Allinea Workshop </span>
+===================================================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified on
+May 19, 2016
+
+<span style="color: rgb(0,0,0);">When: May 20th, 1-2:30PM</span> <span style="color: rgb(0,0,0);">Where: UNL AVH 347 and UNO PKI 250</span>
+-------------------------------------------------------------------------------------------------------------------------------------------
+
+### Untar the files for the examples
+
+The tarball containing the examples is located
+at` /work/demo/SHARED/TrainingTools.tar.gz `on Crane. To unpack them to
+your /work directory, run the following command:
+
+**Unpack the example files to /work**
+
+``` syntaxhighlighter-pre
+tar -zxvf /work/demo/SHARED/TrainingTools.tar.gz -C $WORK
+```
+
+This will create a `TrainingTools `folder in your /work directory with
+the files.
+
+### Setup the Allinea client software to use Reverse Connect
+
+The Allinea DDT/MAP software supports a Reverse Connect feature. The
+GUI is installed and run locally, and information from the job running
+on the cluster is sent back to your laptop/workstation via SSH. This is
+the recommended way to use the software for interactive
+debugging/profiling of a job on HCC resources. Traditional X11
+forwarding will also work, but is not recommended as the interface can
+be much slower to respond. In order to follow along with the demos, use
+these instructions to setup the Allinea client on your laptop.
+
+First, download and install the remote client software for either
+Windows or OS X
+from <a href="https://www.allinea.com/products/forge/download#remote-client" class="external-link">this page</a>.
+Alternatively, download the software directory for your OS:
+ <a href="http://content.allinea.com/downloads/allinea-forge-client-latest-MacOSX-10.7.5-x86_64.dmg" class="external-link">[OS X direct link]</a>
+ <a href="http://content.allinea.com/downloads/allinea-forge-client-latest-Windows-6.1-x64.exe" class="external-link">[Windows 64-bit direct link]</a>
+ <a href="http://content.allinea.com/downloads/allinea-forge-client-latest-Windows-6.1-x86.exe" class="external-link">[Windows 32-bit direct link]</a>
+
+Start the Allinea software, and choose *Configure...* from the *Remote
+Launch* dropdown menu.
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/16515582/16515586.png" class="confluence-embedded-image confluence-content-image-border" width="300" height="78" /></span>
+
+
+Click the *Add* button on the new window.
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/16515582/16515589.png" class="confluence-embedded-image confluence-content-image-border" width="400" height="322" /></span>
+
+
+To setup a connection to Crane, fill in the fields as follows:
+*Connection Name: *Crane
+*Host Name:* <HCC username>@crane.unl.edu
+*Remote Installation Directory:* /util/opt/allinea/6.0
+
+It should appear similar to this:
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/16515582/16515622.png" class="confluence-embedded-image confluence-content-image-border" width="500" height="306" /></span>
+
+Be sure to replace *demo02* with your HCC username.
+
+Click *OK* to close this dialog, and then *Close* on *Configure Remote
+Connections* to return back to the main Allinea window.
+
+Next, log in to Crane. The Allinea software uses a *.allinea *directory
+in your home directory to store configuration information. Since /home
+is read-only from the nodes in the cluster, the directory will be
+created in /work and symlink'd. To do so, run the following commands:
+
+**Create and symlink .allinea directory**
+
+``` syntaxhighlighter-pre
+rm -rf $HOME/.allinea $WORK/.allinea
+mkdir -p $WORK/.allinea
+ln -s $WORK/.allinea $HOME/.allinea
+```
+
+### Test the Reverse Connect feature
+
+To test the connection, choose *Crane* from the *Remote Launch* menu.
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/16515582/16515602.png" class="confluence-embedded-image confluence-content-image-border" width="300" height="114" /></span>
+
+A* Connect to Remote Host* dialog will appear and prompt for a password.
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/16515582/16515603.png" class="confluence-embedded-image confluence-content-image-border" width="500" height="310" /></span>
+
+The login procedure is the same as for PuTTY or any other SSH program.
+ Enter your HCC password followed by the Duo login.
+If the login was successful, you should see *Connected to:
+<username>@crane.unl.edu* in the lower right corner of the Allinea
+window.
+
+The next step is to run a sample interactive job and test the Reverse
+Connect connection. Start an interactive job by running the following
+command.
+
+**Start an interactive job**
+
+``` syntaxhighlighter-pre
+srun --pty --qos=short bash
+```
+
+Once the job has started, load the allinea module and start DDT using
+the `--connect` option.
+
+**Start DDT**
+
+``` syntaxhighlighter-pre
+module load allinea/6.0
+ddt --connect
+```
+
+
+On your local machine, a pop-up box should appear prompting you to
+accept the Reverse Connect request.
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/16515582/16515613.png" class="confluence-embedded-image confluence-content-image-border" width="450" /></span>
+
+Choose *Accept.* The *Remote Launch *section should change to indicate
+you are connected via tunnel, similar to:
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/16515582/16515615.png" class="confluence-embedded-image confluence-thumbnail confluence-content-image-border" width="250" /></span>
+
+Once that happens, Reverse Connect is working successfully and a
+debugging or profiling session can be started.
+
+During the Workshop
+-------------------
+
+### Compiling the examples
+
+In order to compile and run the example programs, an MPI compiler will
+need to be available. For this workshop, it is suggested to use GCC 4.9
+and OpenMPI 1.8. To load those modules, run
+
+**Load compiler modules**
+
+``` syntaxhighlighter-pre
+module load compiler/gcc/4.9 openmpi/1.8 allinea/6.0
+```
+
+Once the modules are loaded, you can run `make` as instructed in the
+various example code folders.
+
+### Starting interactive jobs for serial, OpenMP/pthreads, and MPI code
+
+The `srun `syntax is slightly different depending on which type of code
+you are debugging. Use the following commands to start interactive jobs
+for each type.
+
+**Serial code**
+
+``` syntaxhighlighter-pre
+ srun --pty --time=2:00:00 --reservation=allinea bash
+```
+
+**OpenMP/pthreads code**
+
+``` syntaxhighlighter-pre
+srun --pty --time=2:00:00 --nodes=1 --ntasks-per-node=4 --reservation=allinea bash
+```
+
+**MPI code**
+
+``` syntaxhighlighter-pre
+srun --pty --time=2:00:00 --ntasks=4 --reservation=allinea bash
+```
+
+**Please note that the `--reservation=allinea` option will only work
+during the workshop.**
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
+Shot 2016-05-16 at 11.28.32 AM.png](attachments/16515582/16515586.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
+Shot 2016-05-16 at 11.32.34 AM.png](attachments/16515582/16515591.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
+Shot 2016-05-16 at 11.32.34 AM.png](attachments/16515582/16515589.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
+Shot 2016-05-16 at 11.38.13 AM.png](attachments/16515582/16515595.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
+Shot 2016-05-16 at 12.15.43 PM.png](attachments/16515582/16515602.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
+Shot 2016-05-16 at 12.17.14 PM.png](attachments/16515582/16515605.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
+Shot 2016-05-16 at 12.17.14 PM.png](attachments/16515582/16515603.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
+Shot 2016-05-16 at 12.04.42 PM.png](attachments/16515582/16515643.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
+Shot 2016-05-16 at 12.05.01 PM.png](attachments/16515582/16515615.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
+Shot 2016-05-16 at 11.37.09 AM.png](attachments/16515582/16515622.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
+Shot 2016-05-16 at 12.04.42 PM.png](attachments/16515582/16515613.png)
+(image/png)
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/events/july_2014_bioinformatics_workshop.md b/content/events/july_2014_bioinformatics_workshop.md
new file mode 100644
index 00000000..7e9d0545
--- /dev/null
+++ b/content/events/july_2014_bioinformatics_workshop.md
@@ -0,0 +1,35 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [HCC Events](HCC-Events_332364.html)
+
+<span id="title-text"> HCC-DOCS : July 2014 Bioinformatics Workshop </span>
+===========================================================================
+
+Created by <span class="author"> Jingchao Zhang</span>, last modified on
+Jul 29, 2014
+
+Quick
+link: <a href="http://cse.unl.edu/~bioinfo/workshop/" class="external-link">http://cse.unl.edu/~bioinfo/workshop/</a>
+
+Monday - Wednesday, July 28 -30 (lunch will be provided)
+
+
+
+[Download Workshop Schedule](attachments/8192294/8126551.pdf)
+
+[Download Galaxy101 PowerPoint](attachments/8192294/8126550.pptx)
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[Bioinfo2014\_Galaxy101.pptx](attachments/8192294/8126550.pptx)
+(application/vnd.openxmlformats-officedocument.presentationml.presentation)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[Workshop\_schedule.pdf](attachments/8192294/8126551.pdf)
+(application/pdf)
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/events/june_2013_osg_workshop.md b/content/events/june_2013_osg_workshop.md
new file mode 100644
index 00000000..0827c907
--- /dev/null
+++ b/content/events/june_2013_osg_workshop.md
@@ -0,0 +1,59 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [HCC Events](HCC-Events_332364.html)
+
+<span id="title-text"> HCC-DOCS : June 2013 OSG Workshop </span>
+================================================================
+
+Created by <span class="author"> Derek Weitzel</span>, last modified on
+Aug 02, 2013
+
+Quick
+link: <a href="http://go.unl.edu/hccosg2013" class="external-link">http://go.unl.edu/hccosg2013</a>
+
+Location: <span style="line-height: 1.4285715;">Unity Room/212 in the
+Jackie Gaughan Multicultural Center</span>
+
+| Time | Title | Description |
+|---------|-------------------------------------------------------|------------------------------------------------------------------|
+| 9am | [Intro to HTC](2850830.html) | Introduction to High Throughput Computing |
+| 10:30am | [Practice Blast Job](Practice-Blast-Job_2850818.html) | Run a real science application, Blast, on a Condor based system. |
+| 12pm | Lunch | Lunch is provided. |
+| 1pm | [Workflows](Workflows-in-Condor_2850943.html) | Learn how to describe a workflow in DAG format. |
+| 2pm | [Portability](2850906.html) | Transfer input and output files with the jobs |
+| 3pm | [Big Data](Using-HTTP_2850974.html) | Learn how to handle large data in HTC |
+
+Password for demo account is 'OSG@HCC2013'.
+
+1. <span style="line-height: 1.4285715;">Intro to HTC (A)</span>
+ 1. HTC vs. HPC
+ 2. Submitting HTC jobs
+2. Practice Blast Job (D)
+ 1. input files
+ 2. output files
+ 3. job monitoring - where to look for problems
+ 4. Condor clustering?
+ <span style="line-height: 1.4285715;"><lunch></span>
+3. Dagman (D)
+ 1. Intro to dagman
+ 2. Multiple queries and
+ summarize <a href="https://opensciencegrid.org/bin/view/Education/OSGSS2012CondorBLAST" class="external-link">OSG Page</a>
+4. Portability (A)
+ 1. Compiling for lowest common denominator
+ 2. Data Requirements
+ 3. Packaging (wrapper scripts?)
+ 4. [Example: Running R on the OSG](2850906.html)
+5. Big Data (A)
+ 1. Medium Data 10MB - 500MB - HTTP
+ 2. Large Data 500MB+ - SRM / GridFTP
+ 3. [Example: Using HTTP](Using-HTTP_2850974.html)
+
+
+
+Materials borrowed
+from <a href="https://opensciencegrid.org/bin/view/Education/UserSchool12Materials" class="external-link">OSG</a>.
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/events/june_2014_bioinformatics_workshop.md b/content/events/june_2014_bioinformatics_workshop.md
new file mode 100644
index 00000000..b0bf8af3
--- /dev/null
+++ b/content/events/june_2014_bioinformatics_workshop.md
@@ -0,0 +1,62 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [HCC Events](HCC-Events_332364.html)
+
+<span id="title-text"> HCC-DOCS : June 2014 Bioinformatics Workshop </span>
+===========================================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified on
+Jun 26, 2014
+
+Quick
+link: <a href="http://go.unl.edu/hccbioinfo2014" class="external-link">http://go.unl.edu/hccbioinfo2014</a>
+
+Thursday, June 26 \| 10am-4pm (lunch will be provided)
+
+Filley Hall, Room 302
+
+**Please bring your laptop. This will be a hands-on workshop.**
+
+### Tentative Schedule
+
+| | |
+|--------------|---------------------------------------------------------|
+| 10am-10:45am | intro to HCC, account setup |
+| 10:45am-12pm | intro to linux, basic commands, Globus account setup |
+| 12pm-1pm | lunch (pizza will be provided) |
+| 1pm-1:30pm | editing files with nano |
+| 1:30pm-2pm | cluster basics (SLURM, module), hello world example job |
+| 2pm-4pm | how to run BLAST jobs |
+
+
+
+[Click to download PDF of
+presentation.](attachments/8192150/8126518.pdf)
+
+
+
+[Click to download BLAST presentation](attachments/8192150/8126522.pdf)
+
+
+
+[Click to download example query
+file](attachments/8192150/8126516.query)
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[mouse.query](attachments/8192150/8126516.query)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[HCC\_workshop.pdf](attachments/8192150/8126518.pdf) (application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[HCC\_workshop.ppt](attachments/8192150/8126521.ppt)
+(application/vnd.ms-powerpoint)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[BLAST.pdf](attachments/8192150/8126522.pdf) (application/pdf)
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/events/june_workshop_series_2017.md b/content/events/june_workshop_series_2017.md
new file mode 100644
index 00000000..f50d6521
--- /dev/null
+++ b/content/events/june_workshop_series_2017.md
@@ -0,0 +1,93 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [HCC Events](HCC-Events_332364.html)
+
+<span id="title-text"> HCC-DOCS : June Workshop Series 2017 </span>
+===================================================================
+
+Created by <span class="author"> Carrie Brown</span>, last modified on
+Jul 11, 2017
+
+<a href="https://hcc.unl.edu/june-workshop-series" class="external-link">https://hcc.unl.edu/june-workshop-series</a>
+=====================================================================================================================
+
+**June 6th and 13th: Bash and Git**
+===================================
+
+Learn how to navigate in the Linux command line. Topics include the use
+of pipes, filters, loops, handling text files, and how to write
+reuseable shell scripts to help automate tasks. We will also be looking
+at how using the Git version control system can help streamline
+collaboration and manage revisions. Lesson materials based on Software
+Carpentry lessons.
+
+#### Workshop Materials:
+
+- Links to Lessons:
+ <a href="https://unlhcc.github.io/2017-06-06-UNL/" class="external-link">https://unlhcc.github.io/2017-06-06-UNL/</a>
+- Attendee Portal:
+ <a href="http://hcc.unl.edu/swc-history/index.html" class="external-link">http://hcc.unl.edu/swc-history/index.html</a>
+
+
+**June 20th: Introductory HCC**
+===============================
+
+Learn the basics of working with Holland resources. Topics include an
+overview of HCC offerings, connecting to the clusters, submitting jobs,
+handling data and tips on how to optimize workflow.
+
+#### Workshop Materials:
+
+- Presenter Slides:
+ - [Introduction to HCC.pptx](attachments/18548621/18548623.pptx)
+ - [Introduction to HCC.pdf](attachments/18548621/18548624.pdf)
+- Etherpad:
+ <a href="https://etherpad.wikimedia.org/p/2017_06_20_UNL" class="external-link">https://etherpad.wikimedia.org/p/2017_06_20_UNL</a>
+
+
+**June 27th: All about SLURM**
+==============================
+
+Learn all about the Simple Linux Utility for Resource Management
+(SLURM), HCC's workload manager (scheduler) and how to select the best
+options to streamline your jobs.
+
+#### Workshop Materials:
+
+- Presenter Slides:
+ - [All About Slurm.pptx](attachments/18548621/18549050.pptx)
+ - [All About Slurm.pdf](attachments/18548621/21070067.pdf)
+- Etherpad:
+ <a href="https://etherpad.wikimedia.org/p/2017_06_27_UNL" class="external-link">https://etherpad.wikimedia.org/p/2017_06_27_UNL</a>
+
+
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[Introduction to HCC 2.pptx](attachments/18548621/18548623.pptx)
+(application/vnd.openxmlformats-officedocument.presentationml.presentation)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[Introduction to HCC.pdf](attachments/18548621/18548624.pdf)
+(application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [All
+About Slurm.pdf](attachments/18548621/21070066.pdf) (application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [All
+About Slurm.pptx](attachments/18548621/21070065.pptx)
+(application/vnd.openxmlformats-officedocument.presentationml.presentation)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [All
+About Slurm.pptx](attachments/18548621/18549050.pptx)
+(application/vnd.openxmlformats-officedocument.presentationml.presentation)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [All
+About Slurm.pdf](attachments/18548621/18549049.pdf) (application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [All
+About Slurm pdf.pdf](attachments/18548621/21070067.pdf)
+(application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Intro
+to HCC.pdf](attachments/18548621/33686225.pdf) (application/pdf)
+
+Document generated by Confluence on Oct 24, 2018 14:56
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/events/june_workshop_series_2018.md b/content/events/june_workshop_series_2018.md
new file mode 100644
index 00000000..0bdfde4e
--- /dev/null
+++ b/content/events/june_workshop_series_2018.md
@@ -0,0 +1,32 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [HCC Events](HCC-Events_332364.html)
+
+<span id="title-text"> HCC-DOCS : June Workshop Series 2018 </span>
+===================================================================
+
+Created by <span class="author"> Carrie Brown</span>, last modified by
+<span class="editor"> Emelie Harstad</span> on Jun 26, 2018
+
+Introduction to OSG: [Slides(pdf)](attachments/33689824/33689834.pdf)
+ [Slides(ppt)](attachments/33689824/33689835.pptx)
+
+Introduction to Anvil: [Slides](attachments/33689824/33689825.pdf)
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[Intro\_to\_Anvil.pdf](attachments/33689824/33689825.pdf)
+(application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[OSG\_HCCWorkshop\_20180626.pdf](attachments/33689824/33689834.pdf)
+(application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[OSG\_HCCWorkshop\_20180626.pptx](attachments/33689824/33689835.pptx)
+(application/vnd.openxmlformats-officedocument.presentationml.presentation)
+
+Document generated by Confluence on Oct 24, 2018 14:56
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/events/nebraska_supercomputing_symposium_12.md b/content/events/nebraska_supercomputing_symposium_12.md
new file mode 100644
index 00000000..cf2fc535
--- /dev/null
+++ b/content/events/nebraska_supercomputing_symposium_12.md
@@ -0,0 +1,80 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [HCC Events](HCC-Events_332364.html)
+
+<span id="title-text"> HCC-DOCS : Nebraska Supercomputing Symposium '12 </span>
+===============================================================================
+
+Created by <span class="author"> Derek Weitzel</span>, last modified by
+<span class="editor"> Ashu Guru</span> on Nov 08, 2012
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/332369/622612.jpg?effects=drop-shadow" class="confluence-embedded-image confluence-thumbnail" width="300" /></span><span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/332369/622613.jpg?effects=drop-shadow" class="confluence-embedded-image confluence-thumbnail" width="300" /></span>
+
+Short
+Link: <a href="http://go.unl.edu/nss12" class="external-link">http://go.unl.edu/nss12</a>
+
+Schedule: <a href="http://researchfair.unl.edu/schedule/" class="external-link">http://researchfair.unl.edu/schedule/</a>
+
+<span class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/332369/622606.png" class="confluence-embedded-image confluence-thumbnail" width="100" /></span> Talks
+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+
+- [Intro slides](attachments/332369/622608.pdf)
+- [Carl's Tools Slides](attachments/332369/622605.pdf)
+- [Pivot Grid Presentation](attachments/332369/622618.pdf)
+- [Lark Presentation](attachments/332369/622607.pdf)
+
+HCC Talks
+---------
+
+- [HCC Overview](attachments/332369/622614.pptx)
+- [High Throughput Computing Talk](attachments/332369/622616.pdf)
+- [HCCgo](attachments/332369/622619.pdf)
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[PivotSharing.pptx](attachments/332369/622604.pptx)
+(application/vnd.openxmlformats-officedocument.presentationml.presentation)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[Cluster\_HCC\_2012.pdf](attachments/332369/622605.pdf)
+(application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[PIVOT\_Logo.png](attachments/332369/622606.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[gattebury-lark.pdf](attachments/332369/622607.pdf) (application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[pivot\_2012.pdf](attachments/332369/622608.pdf) (application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[2012-11-07 12.09.31 HDR.jpg](attachments/332369/622610.jpg)
+(image/jpeg)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[2012-11-07 13.03.29 HDR.jpg](attachments/332369/622611.jpg)
+(image/jpeg)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[2012-11-07 13.03.26 copy.jpg](attachments/332369/622612.jpg)
+(image/jpeg)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[2012-11-07 12.09.31 HDR copy.jpg](attachments/332369/622613.jpg)
+(image/jpeg)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[nss12-2.pptx](attachments/332369/622614.pptx)
+(application/vnd.openxmlformats-officedocument.presentationml.presentation)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[HTCTalk.pptx](attachments/332369/622615.pptx)
+(application/vnd.openxmlformats-officedocument.presentationml.presentation)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[HTCTalk.pdf](attachments/332369/622617.pdf) (application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[HTCTalk.pdf](attachments/332369/622616.pdf) (application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[PivotSharing.pdf](attachments/332369/622618.pdf) (application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hccgo.pdf](attachments/332369/622619.pdf) (application/pdf)
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/events/october_2014_hcc_workshop_college_of_engineering.md b/content/events/october_2014_hcc_workshop_college_of_engineering.md
new file mode 100644
index 00000000..457c835c
--- /dev/null
+++ b/content/events/october_2014_hcc_workshop_college_of_engineering.md
@@ -0,0 +1,36 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [HCC Events](HCC-Events_332364.html)
+
+<span id="title-text"> HCC-DOCS : October 2014 HCC Workshop - College of Engineering </span>
+============================================================================================
+
+Created by <span class="author"> Jingchao Zhang</span>, last modified on
+Oct 10, 2014
+
+When: October 10th, 2014 3:00 - 5:00
+
+Where: Scott Engineering Center (SEC) room 357
+
+Materials:
+
+[slides (ppt)](attachments/9470028/9863291.pptx)
+ [PDF](attachments/9470028/9863292.pdf)
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [HCC
+Workshop - Engineering.pdf](attachments/9470028/9863290.pdf)
+(application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [HCC
+Workshop - Engineering.pptx](attachments/9470028/9863291.pptx)
+(application/vnd.openxmlformats-officedocument.presentationml.presentation)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [HCC
+Workshop - Engineering (1).pdf](attachments/9470028/9863292.pdf)
+(application/pdf)
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/events/september_2014_hcc_workshop_earth_and_atmospheric_sciences.md b/content/events/september_2014_hcc_workshop_earth_and_atmospheric_sciences.md
new file mode 100644
index 00000000..7c57aa94
--- /dev/null
+++ b/content/events/september_2014_hcc_workshop_earth_and_atmospheric_sciences.md
@@ -0,0 +1,47 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [HCC Events](HCC-Events_332364.html)
+
+<span id="title-text"> HCC-DOCS : September 2014 HCC Workshop - Earth and Atmospheric Sciences </span>
+======================================================================================================
+
+Created by <span class="author"> Emelie Harstad</span>, last modified on
+Sep 23, 2014
+
+When: September 23rd and 30th, 2014 11:00-12:15
+
+Where: 105 Bessey Hall
+
+<a href="http://hcc.unl.edu/fall-workshop-september-2330-snr-0" class="external-link">Registration Link</a>
+
+<span style="line-height: 1.4285715;">Materials:
+ [slides(ppt)](attachments/8847366/8945736.pptx),
+[slides(pdf)](attachments/8847366/8945737.pdf),
+[matlab\_demo](attachments/8847366/8945735.gz)</span>
+
+<span style="line-height: 1.4285715;">
+</span>
+
+
+
+
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[matlab\_demo.zip](attachments/8847366/8945734.zip) (application/zip)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[matlab\_demo.tar.gz](attachments/8847366/8945735.gz)
+(application/x-gzip)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[HCC\_Workshop\_EAS.pptx](attachments/8847366/8945736.pptx)
+(application/vnd.openxmlformats-officedocument.presentationml.presentation)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[HCC\_Workshop\_EAS.pdf](attachments/8847366/8945737.pdf)
+(application/pdf)
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/events/software_carpentry_open_science_grid_workshop_unl_january_6_8_2016.md b/content/events/software_carpentry_open_science_grid_workshop_unl_january_6_8_2016.md
new file mode 100644
index 00000000..d6d87d00
--- /dev/null
+++ b/content/events/software_carpentry_open_science_grid_workshop_unl_january_6_8_2016.md
@@ -0,0 +1,38 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [HCC Events](HCC-Events_332364.html)
+
+<span id="title-text"> HCC-DOCS : Software Carpentry - Open Science Grid Workshop-UNL, January 6-8, 2016 </span>
+================================================================================================================
+
+Created by <span class="author"> Natasha Pavlovikj</span>, last modified
+on Jun 22, 2016
+
+**When**: January 6-8, 2016
+
+**Where**: UNL Campus, Avery Hall 119
+
+**Quick
+Link**: <a href="https://swc-osg-workshop.github.io/2016-01-06-UNL/" class="external-link">https://swc-osg-workshop.github.io/2016-01-06-UNL/</a>
+
+**Materials**
+=============
+
+**Etherpad**: <a href="https://public.etherpad-mozilla.org/p/2016-01-06-UNL" class="external-link">https://public.etherpad-mozilla.org/p/2016-01-06-UNL</a>
+
+**Shell
+Lesson**: <a href="http://swc-osg-workshop.github.io/2016-01-06-UNL/novice/shell/" class="external-link">http://swc-osg-workshop.github.io/2016-01-06-UNL/novice/shell/</a>
+
+**Git
+Lesson**: <a href="https://eharstad.github.io/git-novice/" class="external-link">https://eharstad.github.io/git-novice/</a>
+
+**Python
+Lesson**: <a href="https://djw8605.github.io/python-novice-inflammation/" class="external-link">https://djw8605.github.io/python-novice-inflammation/</a>
+
+**Open Science Grid
+Lesson**: <a href="http://swc-osg-workshop.github.io/2016-01-06-UNL/novice/DHTC/" class="external-link">http://swc-osg-workshop.github.io/2016-01-06-UNL/novice/DHTC/</a>
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/events/software_carpentry_workshop_setup.md b/content/events/software_carpentry_workshop_setup.md
new file mode 100644
index 00000000..e0b8a247
--- /dev/null
+++ b/content/events/software_carpentry_workshop_setup.md
@@ -0,0 +1,108 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [HCC Events](HCC-Events_332364.html)
+
+<span id="title-text"> HCC-DOCS : Software Carpentry Workshop Setup </span>
+===========================================================================
+
+Created by <span class="author"> Carrie Brown</span>, last modified on
+Aug 06, 2018
+
+For Windows:
+============
+
+Bash/Git
+--------
+
+1. Download
+ <a href="https://git-for-windows.github.io/" class="external-link">Git for Windows </a>
+2. Run the installer, Click "Yes" if prompted to allow the program to
+ make changes.
+ <span
+ class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/35324391/35324402.png" class="confluence-embedded-image" height="250" /></span>
+
+3. Click "Next"
+ <span
+ class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/35324391/35324403.png" class="confluence-embedded-image" height="400" /></span>
+
+4. Click "Next"
+ <span
+ class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/35324391/35324405.png" class="confluence-embedded-image" height="400" /></span>
+
+5. Select "Use the Nano editor by default" and click "Next"
+ <span
+ class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/35324391/35324406.png" class="confluence-embedded-image" height="400" /></span>
+
+6. Ensure "Use Git from the Windows Command Prompt" is selected and
+ click "Next
+ <span
+ class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/35324391/35324407.png" class="confluence-embedded-image" height="400" /></span>
+
+7. Click "Next"
+ <span
+ class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/35324391/35324408.png" class="confluence-embedded-image" height="400" /></span>
+
+8. Ensure "Checkout Windows-style, commit Unix-style line endings" is
+ selected and click "Next"
+ <span
+ class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/35324391/35324409.png" class="confluence-embedded-image" height="400" /></span>
+
+9. Click "Next"
+ <span
+ class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/35324391/35324410.png" class="confluence-embedded-image" height="400" /></span>
+
+10. Click "Install"
+ <span
+ class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/35324391/35324411.png" class="confluence-embedded-image" height="400" /></span>
+
+11. Click "Finish"
+ <span
+ class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/35324391/35324412.png" class="confluence-embedded-image" height="400" /></span>
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2018-8-6\_11-16-17.png](attachments/35324391/35324400.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2018-8-6\_11-16-41.png](attachments/35324391/35324401.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2018-8-6\_11-17-16.png](attachments/35324391/35324402.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2018-8-6\_11-17-41.png](attachments/35324391/35324403.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2018-8-6\_11-18-8.png](attachments/35324391/35324404.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2018-8-6\_11-18-14.png](attachments/35324391/35324405.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2018-8-6\_11-18-55.png](attachments/35324391/35324406.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2018-8-6\_11-19-47.png](attachments/35324391/35324407.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2018-8-6\_11-20-40.png](attachments/35324391/35324408.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2018-8-6\_11-21-8.png](attachments/35324391/35324409.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2018-8-6\_11-21-25.png](attachments/35324391/35324410.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2018-8-6\_11-27-58.png](attachments/35324391/35324411.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2018-8-6\_11-29-23.png](attachments/35324391/35324412.png)
+(image/png)
+
+Document generated by Confluence on Oct 24, 2018 14:56
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/events/software_carpentry_workshop_unl_january_5_6_2017.md b/content/events/software_carpentry_workshop_unl_january_5_6_2017.md
new file mode 100644
index 00000000..b073f2d7
--- /dev/null
+++ b/content/events/software_carpentry_workshop_unl_january_5_6_2017.md
@@ -0,0 +1,55 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [HCC Events](HCC-Events_332364.html)
+
+<span id="title-text"> HCC-DOCS : Software Carpentry Workshop-UNL, January 5-6, 2017 </span>
+============================================================================================
+
+Created by <span class="author"> Natasha Pavlovikj</span>, last modified
+on Jan 05, 2017
+
+**When**: January 5-6, 2017
+
+**Where**: Jackie Gaughan Multicultural Center - room 202 (Ubuntu)
+
+**Quick Link**:
+<a href="https://eharstad.github.io/2017-01-05-UNL" class="external-link">https://eharstad.github.io/2017-01-05-UNL</a>
+
+**Materials**
+=============
+
+**Introduction:**
+
+**<span
+class="confluence-embedded-file-wrapper"><a href="/download/attachments/17041001/SWC-UNL-2017_01_05.pptx?version=1&modificationDate=1483674264000&api=v2" class="confluence-embedded-file"><img src="assets/images/documentConversion/latest/conversion/thumbnail/17041003/1" height="250" /></a></span>**
+
+**<span
+class="confluence-embedded-file-wrapper"><a href="/download/attachments/17041001/SWC-UNL-2017_01_05.pdf?version=1&modificationDate=1483674263000&api=v2" class="confluence-embedded-file"><img src="assets/images/documentConversion/latest/conversion/thumbnail/17041002/1" height="250" /></a></span>
+**
+
+**Etherpad**:
+<a href="https://public.etherpad-mozilla.org/p/2017-01-05-UNL" class="external-link">https://public.etherpad-mozilla.org/p/2017-01-05-UNL</a>
+
+**Shell Lesson**: <span
+style="color: rgb(24,54,145);"> </span><a href="https://eharstad.github.io/shell-novice/" class="external-link">https://eharstad.github.io/shell-novice/</a>
+
+**Git Lesson**: <span
+style="color: rgb(24,54,145);"> </span><a href="https://eharstad.github.io/git-novice/" class="external-link">https://eharstad.github.io/git-novice/</a>
+
+**R Lesson**:<span
+style="color: rgb(24,54,145);"> </span><a href="https://carriebrown.github.io/r-novice-gapminder/" class="external-link">https://carriebrown.github.io/r-novice-gapminder/</a>
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[SWC-UNL-2017\_01\_05.pdf](attachments/17041001/17041002.pdf)
+(application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[SWC-UNL-2017\_01\_05.pptx](attachments/17041001/17041003.pptx)
+(application/vnd.openxmlformats-officedocument.presentationml.presentation)
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/events/software_carpentry_workshop_unl_january_8_9_2015.md b/content/events/software_carpentry_workshop_unl_january_8_9_2015.md
new file mode 100644
index 00000000..7bed7362
--- /dev/null
+++ b/content/events/software_carpentry_workshop_unl_january_8_9_2015.md
@@ -0,0 +1,29 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [HCC Events](HCC-Events_332364.html)
+
+<span id="title-text"> HCC-DOCS : Software Carpentry Workshop-UNL, January 8-9, 2015 </span>
+============================================================================================
+
+Created by <span class="author"> Natasha Pavlovikj</span>, last modified
+on Jun 22, 2016
+
+**When**: January 8-9, 2015
+
+**Where**: UNL Campus, Avery Hall 119
+
+**Quick
+Link**: <a href="http://mckays630.github.io/2015-01-08-unl/" class="external-link">http://mckays630.github.io/2015-01-08-unl/</a>
+
+**<span style="color: rgb(0,0,0);">Materials</span>**
+=====================================================
+
+**Etherpad**: <a href="https://etherpad.mozilla.org/2015-01-08-unl" class="external-link">https://etherpad.mozilla.org/2015-01-08-unl</a>
+
+**Shell, Git, Python
+Lessons**: <a href="https://github.com/mckays630/2015-01-08-unl/tree/gh-pages/unl_lessons" class="external-link">https://github.com/mckays630/2015-01-08-unl/tree/gh-pages/unl_lessons</a>
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/events/software_carpentry_workshop_unl_july_15_16_2015.md b/content/events/software_carpentry_workshop_unl_july_15_16_2015.md
new file mode 100644
index 00000000..c60dd6fa
--- /dev/null
+++ b/content/events/software_carpentry_workshop_unl_july_15_16_2015.md
@@ -0,0 +1,35 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [HCC Events](HCC-Events_332364.html)
+
+<span id="title-text"> HCC-DOCS : Software Carpentry Workshop-UNL, July 15-16, 2015 </span>
+===========================================================================================
+
+Created by <span class="author"> Natasha Pavlovikj</span>, last modified
+on Jun 22, 2016
+
+**When**: July 15-16, 2015
+
+**Where**: UNL Campus, UNL City Union (Regency Suite)
+
+**Quick
+Link**: <a href="http://eharstad.github.io/2015-07-15-UNL/" class="external-link">http://eharstad.github.io/2015-07-15-UNL/</a>
+
+**<span style="color: rgb(0,0,0);">Materials</span>**
+=====================================================
+
+**Etherpad**: <a href="https://etherpad.mozilla.org/2015-07-15" class="external-link">https://etherpad.mozilla.org/2015-07-15</a>
+
+**Shell
+Lesson**: <a href="http://eharstad.github.io/shell-novice/" class="external-link">http://eharstad.github.io/shell-novice/</a>
+
+**Git
+Lesson**: <a href="https://eharstad.github.io/git-novice/" class="external-link">https://eharstad.github.io/git-novice/</a>
+
+**R
+Lesson**: <a href="https://github.com/eharstad/r-novice-inflammation" class="external-link">https://github.com/eharstad/r-novice-inflammation</a>
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/events/software_carpentry_workshop_unl_march_20_21_2015.md b/content/events/software_carpentry_workshop_unl_march_20_21_2015.md
new file mode 100644
index 00000000..e5b7464b
--- /dev/null
+++ b/content/events/software_carpentry_workshop_unl_march_20_21_2015.md
@@ -0,0 +1,35 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [HCC Events](HCC-Events_332364.html)
+
+<span id="title-text"> HCC-DOCS : Software Carpentry Workshop-UNL, March 20-21, 2015 </span>
+============================================================================================
+
+Created by <span class="author"> Natasha Pavlovikj</span>, last modified
+on Jun 22, 2016
+
+**When**: March 20-21, 2015
+
+**Where**: UNL Campus, UNL City Union (Regency Suite) and Avery Hall 119
+
+**Quick
+Link**: <a href="https://jainsley.github.io/2015-03-20-UNL/" class="external-link">https://jainsley.github.io/2015-03-20-UNL/</a>
+
+**<span style="color: rgb(0,0,0);">Materials</span>**
+=====================================================
+
+**Etherpad**: <a href="https://etherpad.mozilla.org/2015-03-20-UNL" class="external-link">https://etherpad.mozilla.org/2015-03-20-UNL</a>
+
+**Shell
+Lesson**: <a href="http://eharstad.github.io/shell-novice/" class="external-link">http://eharstad.github.io/shell-novice/</a>
+
+**Git
+Lesson**: <a href="https://eharstad.github.io/git-novice/" class="external-link">https://eharstad.github.io/git-novice/</a>
+
+**R
+Lesson**: <a href="https://jainsley.github.io/r-novice-inflammation/" class="external-link">https://jainsley.github.io/r-novice-inflammation/</a>
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/events/software_carpentry_workshop_unl_march_27_28_2017.md b/content/events/software_carpentry_workshop_unl_march_27_28_2017.md
new file mode 100644
index 00000000..4b6da82f
--- /dev/null
+++ b/content/events/software_carpentry_workshop_unl_march_27_28_2017.md
@@ -0,0 +1,64 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [HCC Events](HCC-Events_332364.html)
+
+<span id="title-text"> HCC-DOCS : Software Carpentry Workshop-UNL, March 27-28, 2017 </span>
+============================================================================================
+
+Created by <span class="author"> Carrie Brown</span>, last modified by
+<span class="editor"> Emelie Harstad</span> on Mar 29, 2017
+
+**When**: March 27-28, 2017
+
+**Where**: Nebraska Union - Colonial A&B
+
+**Quick Link**:
+<a href="https://unlhcc.github.io/2017-03-27-UNL/" class="external-link">https://unlhcc.github.io/2017-03-27-UNL/</a>
+
+**Materials**
+=============
+
+**
+**
+
+**
+**
+
+**
+**
+
+**Etherpad**:
+<a href="http://pad.software-carpentry.org/2017_03_27_UNL" class="external-link">http://pad.software-carpentry.org/2017_03_27_UNL</a>
+
+**Intro
+Slides: [SWC-UNL-20170327.pdf](attachments/17043687/17043692.pdf)**
+
+**Shell Log:**
+<a href="http://hcc.unl.edu/swc-history/20170327.html" class="external-link">http://hcc.unl.edu/swc-history/20170327.html</a>
+
+**Shell Lesson**: <span
+style="color: rgb(24,54,145);"> </span><a href="https://eharstad.github.io/shell-novice/" class="external-link">https://eharstad.github.io/shell-novice/</a>
+
+**Git Lesson**: <span
+style="color: rgb(24,54,145);"> </span><a href="https://eharstad.github.io/git-novice/" class="external-link">https://eharstad.github.io/git-novice/</a>
+
+**Python Lesson**:<span
+style="color: rgb(24,54,145);"> </span><a href="https://djw8605.github.io/python-novice-inflammation/" class="external-link">https://djw8605.github.io/python-novice-inflammation/</a>
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[SWC-UNL-2017\_01\_05.pptx](attachments/17043687/17043685.pptx)
+(application/vnd.openxmlformats-officedocument.presentationml.presentation)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[SWC-UNL-2017\_01\_05.pdf](attachments/17043687/17043686.pdf)
+(application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[SWC-UNL-20170327.pdf](attachments/17043687/17043692.pdf)
+(application/pdf)
+
+Document generated by Confluence on Oct 24, 2018 14:56
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/events/software_carpentry_workshop_unl_november_5_6_2015.md b/content/events/software_carpentry_workshop_unl_november_5_6_2015.md
new file mode 100644
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+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [HCC Events](HCC-Events_332364.html)
+
+<span id="title-text"> HCC-DOCS : Software Carpentry Workshop-UNL, November 5-6, 2015 </span>
+=============================================================================================
+
+Created by <span class="author"> Natasha Pavlovikj</span>, last modified
+on Jun 22, 2016
+
+**When**: November 5-6, 2015
+
+**Where**: <span style="color: rgb(3,3,3);">Whittier Research Center,
+R</span><span style="color: rgb(3,3,3);">oom 136</span>
+
+**Quick
+Link**: <a href="https://eharstad.github.io/2015-11-05-UNL/" class="external-link">https://eharstad.github.io/2015-11-05-UNL/</a>
+
+**Materials**
+=============
+
+**Etherpad**: <a href="https://public.etherpad-mozilla.org/p/UNL-11-06-2015" class="external-link">https://public.etherpad-mozilla.org/p/UNL-11-06-2015</a>
+
+**Shell
+Lesson**: <a href="http://eharstad.github.io/shell-novice/" class="external-link">http://eharstad.github.io/shell-novice/</a>
+
+**Git
+Lesson**: <a href="https://eharstad.github.io/git-novice/" class="external-link">https://eharstad.github.io/git-novice/</a>
+
+**R
+Lesson**: <a href="https://github.com/jainsley/r-novice-gapminder" class="external-link">https://github.com/jainsley/r-novice-gapminder</a>
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/events/software_carpentry_workshop_uno_april_22_23_2015.md b/content/events/software_carpentry_workshop_uno_april_22_23_2015.md
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+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [HCC Events](HCC-Events_332364.html)
+
+<span id="title-text"> HCC-DOCS : Software Carpentry Workshop-UNO, April 22-23, 2015 </span>
+============================================================================================
+
+Created by <span class="author"> Natasha Pavlovikj</span>, last modified
+on Jun 22, 2016
+
+**When**: April 22-23, 2015
+
+**Where**: UNO Campus, PKI 158
+
+**Quick
+Link**: <a href="http://eharstad.github.io/2015-04-22-UNO/" class="external-link">http://eharstad.github.io/2015-04-22-UNO/</a>
+
+**<span style="color: rgb(0,0,0);">Materials</span>**
+=====================================================
+
+**Etherpad**: <a href="https://etherpad.mozilla.org/2015-04-22-UNO" class="external-link">https://etherpad.mozilla.org/2015-04-22-UNO</a>
+
+**Shell
+Lesson**: <a href="http://eharstad.github.io/shell-novice/" class="external-link">http://eharstad.github.io/shell-novice/</a>
+
+**Git
+Lesson**: <a href="https://eharstad.github.io/git-novice/" class="external-link">https://eharstad.github.io/git-novice/</a>
+
+**Python
+Lesson**: <a href="https://eharstad.github.io/python-novice-inflammation/" class="external-link">https://eharstad.github.io/python-novice-inflammation/</a>
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/events/software_carpentry_workshop_uno_july_14_15_2016.md b/content/events/software_carpentry_workshop_uno_july_14_15_2016.md
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+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [HCC Events](HCC-Events_332364.html)
+
+<span id="title-text"> HCC-DOCS : Software Carpentry Workshop-UNO, July 14-15, 2016 </span>
+===========================================================================================
+
+Created by <span class="author"> Natasha Pavlovikj</span>, last modified
+by <span class="editor"> Jingchao Zhang</span> on Jul 13, 2016
+
+**When**: July 14-15, 2016
+
+**Where**: UNO Campus, PKI 160
+
+**Quick
+Link**: <a href="https://npavlovikj.github.io/2016-07-14-UNO/" class="external-link">https://npavlovikj.github.io/2016-07-14-UNO/</a>
+
+**Materials**
+=============
+
+**Etherpad**: <a href="https://public.etherpad-mozilla.org/p/2016-07-14-UNO" class="external-link">https://public.etherpad-mozilla.org/p/2016-07-14-UNO</a>
+
+**Shell Lesson**: <span
+style="color: rgb(24,54,145);"><a href="http://swcarpentry.github.io/shell-novice/" class="external-link">http://swcarpentry.github.io/shell-novice/</a></span>
+
+**Git Lesson**: <span
+style="color: rgb(24,54,145);"><a href="http://swcarpentry.github.io/shell-novice/" class="external-link">http://swcarpentry.github.io/git-novice/</a></span>
+
+**HCC Lesson**:
+
+<span
+class="confluence-embedded-file-wrapper"><a href="/download/attachments/16516359/2016_July_SWC.pdf?version=2&modificationDate=1468447785000&api=v2" class="confluence-embedded-file"><img src="assets/images/documentConversion/latest/conversion/thumbnail/16517045/2" height="250" /></a></span>
+
+**Python Lesson**: <span
+style="color: rgb(24,54,145);"><a href="https://djw8605.github.io/python-novice-inflammation/" class="external-link">https://djw8605.github.io/python-novice-inflammation/</a></span>
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[2016\_July\_SWC.pdf](attachments/16516359/16517222.pdf)
+(application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[matlab\_demo.tar.gz](attachments/16516359/16517221.gz)
+(application/x-gzip)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[matlab\_demo.tar.gz](attachments/16516359/16517220.gz)
+(application/x-gzip)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[2016\_July\_SWC.pdf](attachments/16516359/16517045.pdf)
+(application/pdf)
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/events/supercomputing_mini_workshop_2012.md b/content/events/supercomputing_mini_workshop_2012.md
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+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [HCC Events](HCC-Events_332364.html)
+
+<span id="title-text"> HCC-DOCS : Supercomputing Mini Workshop 2012 </span>
+===========================================================================
+
+Created by <span class="author"> Derek Weitzel</span>, last modified by
+<span class="editor"> Huang Cheng-Wei</span> on Jul 17, 2013
+
+Quick
+Link: <a href="http://go.unl.edu/supercomputing_mini_2012" class="external-link">http://go.unl.edu/supercomputing_mini_2012</a>
+
+Presentation
+============
+
+[Workshop Presentation](attachments/819232/1114114.pdf)
+
+Materials
+=========
+
+Submit files, code source files, and example scripts can be found in
+the [workshop materials](attachments/819232/1179649.zip).
+
+
+
+
+
+
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[presentation.pdf](attachments/819232/1114114.pdf) (application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[getting\_started.zip](attachments/819232/1179649.zip)
+(application/zip)
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/events/supercomputing_mini_workshop_february_27_2013.md b/content/events/supercomputing_mini_workshop_february_27_2013.md
new file mode 100644
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--- /dev/null
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+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [HCC Events](HCC-Events_332364.html)
+
+<span id="title-text"> HCC-DOCS : Supercomputing Mini Workshop - February 27, 2013 </span>
+==========================================================================================
+
+Created by <span class="author"> Derek Weitzel</span>, last modified on
+Feb 27, 2013
+
+Supercomputing Mini Workshop - February 27, 2013
+================================================
+
+In this hour-long mini workshop, you will obtain hands-on experience
+performing a simple calculation (summing from 1 to 16) with a
+supercomputer, using both serial and parallel computing. No prior
+knowledge of programing is required. The only thing you need to do is
+follow the cheat sheets step by step (copy & paste)! We aim to give the
+framework of the standard supercomputing process and demonstrate that it
+does not require huge efforts for one to take advantage of
+state-of-the-art supercomputing resources.
+
+**Table of Contents
+**
+
+- [Preparation](#SupercomputingMiniWorkshop-February27,2013-Preparation)
+- [Serial Job](#SupercomputingMiniWorkshop-February27,2013-SerialJob)
+- [Parallel
+ Job ](#SupercomputingMiniWorkshop-February27,2013-ParallelJob)
+- [Useful
+ Commands](#SupercomputingMiniWorkshop-February27,2013-UsefulCommands)
+
+**Logging In**
+
+``` syntaxhighlighter-pre
+ssh tusker.unl.edu -l demoXXXX
+```
+
+**<a href="http://cygwin.com/install.html" class="external-link">Cygwin Link</a>**
+
+Preparation
+-----------
+
+**[Download](attachments/1246451/1179891.zip) the demo code.**
+
+Copy the two folders to the clipboard
+
+1. <span
+ style="font-size: 10.0pt;line-height: 13.0pt;">/getting\_started/hcc\_tusker/serial\_f90</span>
+2. /getting\_started/hcc\_tusker/parallel\_f90
+
+On your local computer:
+
+``` syntaxhighlighter-pre
+$ cd ~
+$ mkdir demo_code
+```
+
+Next, search in your computer for the folder “demo\_code”, and paste the
+two folders, serial\_f90 and parallel\_f90, in this folder
+
+``` syntaxhighlighter-pre
+$ ls
+$ scp -r ./demo_code <username>@tusker.unl.edu:/work/demo/<username>
+<enter password>
+```
+
+Serial Job
+----------
+
+First, you need to login to the cluster
+<a href="/pages/createpage.action?spaceKey=HCCDOC&title=Tusker+Cluster&linkCreation=true&fromPageId=1246451" class="createlink">Tusker</a>:
+
+``` syntaxhighlighter-pre
+$ ssh <username>@tusker.unl.edu
+<enter password>
+```
+
+<span style="font-size: 10.0pt;line-height: 13.0pt;">Next, you will move
+to the working filesystem:</span>
+
+``` syntaxhighlighter-pre
+$ cd /work/demo/<username>
+$ ls
+$ cd demo_code
+$ ls
+$ cd serial_f90
+$ ls
+```
+
+Now, load the compiler configuration:
+
+``` syntaxhighlighter-pre
+$ module load compiler/intel/12
+```
+
+And compile the fortran code:
+
+``` syntaxhighlighter-pre
+$ ifort fortran_serial.f90 -o fortran_serial.x
+```
+
+ Next, you will submit the job to the cluster scheduler using a file
+`submit_tusker.serial`. After submitting the job, the cluster will
+schedule your job to run on a node in the cluster.
+
+``` syntaxhighlighter-pre
+$ qsub submit_tusker.serial
+```
+
+<span style="font-size: 10.0pt;line-height: 13.0pt;"> </span><span
+style="font-size: 10.0pt;line-height: 13.0pt;">You can watch the status
+of the job using showq
+(<a href="/pages/createpage.action?spaceKey=HCCDOC&title=Job+Control&linkCreation=true&fromPageId=1246451" class="createlink">reference</a>): </span>
+
+``` syntaxhighlighter-pre
+$ showq -u username
+```
+
+After the job has completed, it will disappear from the showq command.
+ You can check the output of the program from demo.out:
+
+``` syntaxhighlighter-pre
+$ cat demo.out
+```
+
+Parallel Job
+-------------
+
+Again, logged into the cluster as in the Serial job, change to the
+working directory:<span
+style="font-size: 10.0pt;line-height: 13.0pt;"> </span>
+
+``` syntaxhighlighter-pre
+$ cd /work/demo/<username>/demo_code/parallel_f90
+$ ls
+```
+
+<span style="font-size: 10.0pt;line-height: 13.0pt;">Then load both the
+compiler and the MPI (Message Passing Interface) for parallel
+applications.</span>
+
+``` syntaxhighlighter-pre
+$ module load compiler/intel/12
+$ module load openmpi/1.6
+```
+
+Next, you will compile the special parallelized version of the summation
+code. It uses MPI for communication between the parallel processes.
+
+``` syntaxhighlighter-pre
+$ mpif90 fortran_mpi.f90 -o fortran_mpi.x
+```
+
+Next, we will submit the MPI application to the Tusker cluster scheduler
+using the file `submit_tusker.mpi`.
+
+``` syntaxhighlighter-pre
+$ qsub submit_tusker.mpi
+```
+
+The Tusker cluster scheduler will pick machines (possibly several,
+depending on availability) to run the parallel MPI application. You can
+check the status of the job the same way you did with the Serial job:
+
+``` syntaxhighlighter-pre
+$ showq -u <username>
+```
+
+Once you see the job has disappeared from the output of `showq`, you can
+look at the output using the command:
+
+``` syntaxhighlighter-pre
+$ cat demo.out
+```
+
+Useful Commands
+---------------
+
+| Command | Description |
+|-----------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| $ pwd | Print Working Directory - Show the directory that you are currently working in. |
+| $ cd <directory> | Change Directory - Change the working directory to another. |
+| $ cd .. | Change Directory to the one above the current. |
+| $ cat <filename> | Print the contents of a file |
+| $ showq -u <username> | Show the status of jobs for user <username>. (<a href="/pages/createpage.action?spaceKey=HCCDOC&title=Job+Control&linkCreation=true&fromPageId=1246451" class="createlink">reference</a>) |
+| $ qdel <jobid> | Remove the job <jobid> from the queue. Stop job if it is running. |
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_tusker.zip](attachments/1246451/1179891.zip) (application/zip)
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/events/unk_linear_algebra_feb_28th_2017.md b/content/events/unk_linear_algebra_feb_28th_2017.md
new file mode 100644
index 00000000..eae2dc87
--- /dev/null
+++ b/content/events/unk_linear_algebra_feb_28th_2017.md
@@ -0,0 +1,270 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [HCC Events](HCC-Events_332364.html)
+
+<span id="title-text"> HCC-DOCS : UNK: Linear Algebra - Feb 28th, 2017 </span>
+==============================================================================
+
+Created by <span class="author"> Carrie Brown</span>, last modified on
+Feb 27, 2017
+
+**If at any time today you have difficulties or become lost, please
+place the <span style="color: rgb(255,0,0);">red</span> sticky note on
+top of your monitor and a helper will be around to assist you.**
+
+ For these instructions, any commands to be typed into the terminal will be formatted like this.
+
+**What is a cluster:**
+----------------------
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/17042185/17042191.png" class="confluence-embedded-image" width="700" height="307" /></span>
+
+(picture courtesy of:
+<a href="http://training.h3abionet.org/technical_workshop_2015/?page_id=403" class="external-link">http://training.h3abionet.org/technical_workshop_2015/?page_id=403</a>)
+
+**
+**
+
+**To connect to the Crane cluster:**
+------------------------------------
+
+- insert the Yubikey into the computer's USB drive. There should be a
+ small green light in the middle of the Yubikey to indicate it is
+ inserted correctly.
+- Open your preferred web browser and navigate to
+ <a href="http://go.unl.edu/cranessh" class="external-link">http://go.unl.edu/cranessh</a>
+- Click "Start SSH session to crane.unl.edu"
+ <span
+ class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/17042185/17042178.png" class="confluence-embedded-image" height="400" /></span>
+- Click the "Terminal: SSH" icon to begin the SSH session
+ <span
+ class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/17042185/17042179.png" class="confluence-embedded-image" height="400" /></span>
+- Type in the provided Username and Password. Note that the password
+ will not display on screen, but rest assured that even though
+ nothing is being output, your password is being entered as you type.
+- At the "Passcode:" prompt, press your finger to the gold circle in
+ the middle of the Yubikey until a string of characters appears on
+ screen.
+ <span
+ class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/17042185/17042182.png" class="confluence-embedded-image" height="400" /></span>
+- If you logged in successfully, your screen should look similar to
+ the one belo
+ <span
+ class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/17042185/17042183.png" class="confluence-embedded-image" height="400" /></span>
+
+**Linux Commands Reference List:**
+----------------------------------
+
+<table>
+<colgroup>
+<col style="width: 33%" />
+<col style="width: 33%" />
+<col style="width: 33%" />
+</colgroup>
+<thead>
+<tr class="header">
+<th>Command</th>
+<th>What it does</th>
+<th>Example Uses</th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td>ls</td>
+<td>list: Lists the files and directories located in the current directory</td>
+<td><ul>
+<li>ls</li>
+<li>ls -a
+<ul>
+<li>shows all the files in the directory, including hidden ones</li>
+</ul></li>
+<li>ls -l
+<ul>
+<li>shows contents in a list format including information such as file size, file permissions and date the file was modified</li>
+</ul></li>
+<li>ls *.txt
+<ul>
+<li>shows all files in the current directory which end with .txt</li>
+</ul></li>
+</ul></td>
+</tr>
+<tr class="even">
+<td>cd</td>
+<td>change directory: this allows users to in or out of file directories</td>
+<td><ul>
+<li>cd <folder path></li>
+<li>cd folder_name
+<ul>
+<li>navigates into directory "folder_name" located in the current directory</li>
+</ul></li>
+<li>cd ..
+<ul>
+<li>navigates out of a directory and into the parent directory</li>
+</ul>
+cd $HOME (or $WORK)
+<ul>
+<li>navigates to a user's home (or work) directory</li>
+</ul></li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td>mv</td>
+<td>move: used to move a file or directory to another location</td>
+<td><ul>
+<li>mv <current file(s)> <target file(s)></li>
+<li>mv * ../
+<ul>
+<li>moves all files from the current directory into the parent directory</li>
+</ul></li>
+<li>mv old_filename new_filename
+<ul>
+<li>renames the file "old_filename" to "new_filename"</li>
+</ul></li>
+</ul></td>
+</tr>
+<tr class="even">
+<td>man</td>
+<td><p>manual: displays documentation for commands</p>
+<p><strong>Note:</strong> Use up and down arrows to scroll through the text. To exit the manual display, press 'q'</p></td>
+<td><ul>
+<li>man <command name></li>
+<li>man ls
+<ul>
+<li>displays documentation for the ls command</li>
+</ul></li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td>mkdir</td>
+<td>make directory: creates a directory with the specified name</td>
+<td><ul>
+<li>mkdir <new_folder>
+<ul>
+<li>creates the directory "new_folder" within the current directory</li>
+</ul></li>
+</ul></td>
+</tr>
+<tr class="even">
+<td>rmdir</td>
+<td><p>remove directory: deletes a directory with the specified name</p>
+<p><strong>Note:</strong> rmdir only works on empty directories</p></td>
+<td><ul>
+<li>rmdir <folder_name>
+<ul>
+<li>removes the directory "folder_name" if the directory</li>
+</ul></li>
+<li>rmdir *
+<ul>
+<li>removes all directories within the current directory</li>
+</ul></li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td>rm</td>
+<td>remove: deletes file or files with the specified name(s)</td>
+<td><ul>
+<li>rm <file_name>
+<ul>
+<li>deletes the file "file_name"</li>
+</ul></li>
+<li>rm *
+<ul>
+<li>deletes all files in the current directory</li>
+</ul></li>
+</ul></td>
+</tr>
+<tr class="even">
+<td><p>nano</p></td>
+<td><p>nano text editor: opens the nano text editor</p>
+<p><strong>Note:</strong> To access the menu options, ^ indicates the control (CTRL) key.</p></td>
+<td><ul>
+<li>nano
+<ul>
+<li>opens the text editor in a blank file</li>
+</ul></li>
+<li>nano <file_name>
+<ul>
+<li>opens the text editor with "file_name" open. If "file_name" does not exist, it will be created if the file is saved</li>
+</ul></li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td>clear</td>
+<td>clear: clears the screen of all input/output</td>
+<td><ul>
+<li>clear</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td>less</td>
+<td><p>less: opens an extended view of a file</p>
+<p><strong>Note:</strong> Use up and down arrows to scroll through the text. To exit the extended view, press 'q'</p></td>
+<td><ul>
+<li>less <file_name>
+<ul>
+<li>opens an extended view of the file "file_name"</li>
+</ul></li>
+</ul></td>
+</tr>
+</tbody>
+</table>
+
+**To run MATLAB interactively:**
+--------------------------------
+
+- After logging into the cluster, navigate to your $WORK directory:
+ - cd $WORK
+
+- Request an interactive job:
+ - srun --reservation=unk --mem=4096 --pty $SHELL
+
+- Load the MATLAB module:
+ - module load matlab
+
+- Run MATLAB:
+ - matlab
+
+**To access the MATLAB Tutorial:**
+----------------------------------
+
+- Navigate to your $WORK directory:
+ - cd $WORK
+
+- Clone the github repo containing the tutorial files:
+ - git clone https://github.com/unlhcc/HCCWorkshops.git
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
+Shot 2017-02-23 at 5.10.31 PM.png](attachments/17042185/17042180.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
+Shot 2017-02-23 at 5.10.43 PM.png](attachments/17042185/17042181.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
+Shot 2017-02-23 at 5.10.31 PM.png](attachments/17042185/17042178.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
+Shot 2017-02-23 at 5.10.43 PM.png](attachments/17042185/17042179.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
+Shot 2017-02-23 at 5.16.10 PM.png](attachments/17042185/17042182.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
+Shot 2017-02-23 at 5.16.37 PM.png](attachments/17042185/17042184.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
+Shot 2017-02-23 at 5.16.37 PM.png](attachments/17042185/17042183.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2017-2-24 11:14:4.png](attachments/17042185/17042186.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[cluster\_small2.png](attachments/17042185/17042191.png) (image/png)
+
+Document generated by Confluence on Oct 24, 2018 14:56
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/events/unl_numerical_analysis_class_august_5th_2016.md b/content/events/unl_numerical_analysis_class_august_5th_2016.md
new file mode 100644
index 00000000..c06103ea
--- /dev/null
+++ b/content/events/unl_numerical_analysis_class_august_5th_2016.md
@@ -0,0 +1,31 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [HCC Events](HCC-Events_332364.html)
+
+<span id="title-text"> HCC-DOCS : UNL Numerical Analysis Class, August 5th, 2016 </span>
+========================================================================================
+
+Created by <span class="author"> Jingchao Zhang</span>, last modified on
+Aug 04, 2016
+
+Time: 08/05/2016 09:15 am
+
+Location: UNL Avery Room 111
+
+Slides:
+
+<span
+class="confluence-embedded-file-wrapper"><a href="/download/attachments/16517815/2016-August.pdf?version=2&modificationDate=1470358211000&api=v2" class="confluence-embedded-file"><img src="assets/images/documentConversion/latest/conversion/thumbnail/16517814/2" height="250" /></a></span>
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[2016-August.pdf](attachments/16517815/16517817.pdf) (application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[2016-August.pdf](attachments/16517815/16517814.pdf) (application/pdf)
+
+Document generated by Confluence on Oct 24, 2018 14:56
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/events/unl_r_for_biologists_class_march_8_2017.md b/content/events/unl_r_for_biologists_class_march_8_2017.md
new file mode 100644
index 00000000..57acd690
--- /dev/null
+++ b/content/events/unl_r_for_biologists_class_march_8_2017.md
@@ -0,0 +1,311 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [HCC Events](HCC-Events_332364.html)
+
+<span id="title-text"> HCC-DOCS : UNL: R for Biologists Class - March 8, 2017 </span>
+=====================================================================================
+
+Created by <span class="author"> Carrie Brown</span>, last modified on
+Mar 08, 2017
+
+**We will be utilizing <span style="color: rgb(255,0,0);">red</span> and
+<span style="color: rgb(51,153,102);">green</span> sticky notes today.
+If you run into problems or have questions,**
+
+**please place the <span style="color: rgb(255,0,0);">red</span> sticky
+note to the back of your computer screen and a helper will assist you.**
+
+
+
+If you have not already requested an HCC account under the rcourse998
+group, please do so
+here: <a href="https://hcc.unl.edu/new-user-request" class="external-link">https://hcc.unl.edu/new-user-request</a>
+
+If you already have an HCC account and need to be added to the
+rcourse998 group, please let us know.
+
+If you have not previously set up Duo Authentication, please ask for
+assistance.
+
+
+
+**Set up Instructions:**
+
+**Windows:**
+
+For Windows will we use two third party
+application **PuTTY** and **WinSCP** for demonstration.
+
+PuTTY:
+<[putty-0.62-installer.exe](https://hcc-docs.unl.edu/download/attachments/2851288/putty-0.62-installer.exe?version=1&modificationDate=1371067913000&api=v2) or <a href="http://www.putty.org/" class="external-link">http://www.putty.org/</a>>
+
+WinSCP:
+<[winscp515setup.exe](https://hcc-docs.unl.edu/download/attachments/2851288/winscp515setup.exe?version=1&modificationDate=1371155133000&api=v2) or <a href="http://winscp.net/eng/download.php" class="external-link">http://winscp.net/eng/download.php</a>>.
+
+**Mac/Linux:**
+
+Mac and Linux users will need to download and install **Cyberduck**.
+Detailed information for downloading and setting up Cyberduck can be
+found here: [For Mac/Linux Users](2851290.html)
+
+
+
+**R core and R Studio:**
+
+We will be writing scripts offline in RStudio and then uploading them to
+execute them on the cluster. This lesson assumes you have the R core and
+RStudio installed. If you do not you can install them here:
+
+R
+core: <a href="https://cloud.r-project.org/" class="external-link">https://cloud.r-project.org/</a>
+
+RStudio: <a href="https://www.rstudio.com/products/rstudio/download/" class="external-link">https://www.rstudio.com/products/rstudio/download/</a>
+
+
+
+**Required Packages:**
+
+We will also be using the dplyr, ggplot2 and maps package. If you do not
+have these installed, please install them now. You can do so using the
+following commands inside the RStudio console:
+
+ install.packages("dplyr")
+
+ install.packages("ggplot2")
+
+ install.packages("maps")
+
+
+
+**What is a cluster:**
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/17042692/17042703.png" class="confluence-embedded-image" width="700" height="307" /></span></span>
+
+(picture courtesy
+of: <a href="http://training.h3abionet.org/technical_workshop_2015/?page_id=403" class="external-link">http://training.h3abionet.org/technical_workshop_2015/?page_id=403</a>)
+
+
+
+**Linux Commands Reference List:**
+----------------------------------
+
+<table>
+<colgroup>
+<col style="width: 33%" />
+<col style="width: 33%" />
+<col style="width: 33%" />
+</colgroup>
+<thead>
+<tr class="header">
+<th><div class="tablesorter-header-inner">
+Command
+</div></th>
+<th><div class="tablesorter-header-inner">
+What it does
+</div></th>
+<th><div class="tablesorter-header-inner">
+Example Uses
+</div></th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td>ls</td>
+<td>list: Lists the files and directories located in the current directory</td>
+<td><ul>
+<li>ls</li>
+<li>ls -a
+<ul>
+<li>shows all the files in the directory, including hidden ones</li>
+</ul></li>
+<li>ls -l
+<ul>
+<li>shows contents in a list format including information such as file size, file permissions and date the file was modified</li>
+</ul></li>
+<li>ls *.txt
+<ul>
+<li>shows all files in the current directory which end with .txt</li>
+</ul></li>
+</ul></td>
+</tr>
+<tr class="even">
+<td>cd</td>
+<td>change directory: this allows users to in or out of file directories</td>
+<td><ul>
+<li>cd <folder path></li>
+<li>cd folder_name
+<ul>
+<li>navigates into directory "folder_name" located in the current directory</li>
+</ul></li>
+<li>cd ..
+<ul>
+<li>navigates out of a directory and into the parent directory</li>
+</ul>
+cd $HOME (or $WORK)
+<ul>
+<li>navigates to a user's home (or work) directory</li>
+</ul></li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td>mv</td>
+<td>move: used to move a file or directory to another location</td>
+<td><ul>
+<li>mv <current file(s)> <target file(s)></li>
+<li>mv * ../
+<ul>
+<li>moves all files from the current directory into the parent directory</li>
+</ul></li>
+<li>mv old_filename new_filename
+<ul>
+<li>renames the file "old_filename" to "new_filename"</li>
+</ul></li>
+</ul></td>
+</tr>
+<tr class="even">
+<td>man</td>
+<td><p>manual: displays documentation for commands</p>
+<p><strong>Note:</strong> Use up and down arrows to scroll through the text. To exit the manual display, press 'q'</p></td>
+<td><ul>
+<li>man <command name></li>
+<li>man ls
+<ul>
+<li>displays documentation for the ls command</li>
+</ul></li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td>mkdir</td>
+<td>make directory: creates a directory with the specified name</td>
+<td><ul>
+<li>mkdir <new_folder>
+<ul>
+<li>creates the directory "new_folder" within the current directory</li>
+</ul></li>
+</ul></td>
+</tr>
+<tr class="even">
+<td>rmdir</td>
+<td><p>remove directory: deletes a directory with the specified name</p>
+<p><strong>Note: </strong>rmdir only works on empty directories</p></td>
+<td><ul>
+<li>rmdir <folder_name>
+<ul>
+<li>removes the directory "folder_name" if the directory</li>
+</ul></li>
+<li>rmdir *
+<ul>
+<li>removes all directories within the current directory</li>
+</ul></li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td>rm</td>
+<td>remove: deletes file or files with the specified name(s)</td>
+<td><ul>
+<li>rm <file_name>
+<ul>
+<li>deletes the file "file_name"</li>
+</ul></li>
+<li>rm *
+<ul>
+<li>deletes all files in the current directory</li>
+</ul></li>
+</ul></td>
+</tr>
+<tr class="even">
+<td><p>nano</p></td>
+<td><p>nano text editor: opens the nano text editor</p>
+<p><strong>Note: </strong>To access the menu options, ^ indicates the control (CTRL) key.</p></td>
+<td><ul>
+<li>nano
+<ul>
+<li>opens the text editor in a blank file</li>
+</ul></li>
+<li>nano <file_name>
+<ul>
+<li>opens the text editor with "file_name" open. If "file_name" does not exist, it will be created if the file is saved</li>
+</ul></li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td>clear</td>
+<td>clear: clears the screen of all input/output</td>
+<td><ul>
+<li>clear</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td>less</td>
+<td><p>less: opens an extended view of a file</p>
+<p><strong>Note: </strong>Use up and down arrows to scroll through the text. To exit the extended view, press 'q'</p></td>
+<td><ul>
+<li>less <file_name>
+<ul>
+<li>opens an extended view of the file "file_name"</li>
+</ul></li>
+</ul></td>
+</tr>
+</tbody>
+</table>
+
+
+
+### To download the tutorial files:
+
+- Navigate to your $WORK directory:
+ - cd $WORK
+
+- Clone the github repo containing the tutorial files:
+ - git clone https://github.com/unlhcc/HCCWorkshops.git
+
+
+
+Take Home Exercise:
+
+[Data Analysis in R](attachments/17042692/17042690.pdf) - Please note
+that the on the bottom of page three, there is a missing parenthesis at
+the end of the last command.
+
+The final code chunk should read:
+
+ # Calculate flight age using birthmonth
+
+ age <- data.frame(names(acStart), acStart, stringsAsFactors=FALSE)
+
+ colnames(age) <- c("TailNum", "acStart")
+
+ flights <- left_join(flights, age, by="TailNum")
+
+ flights <- mutate(flights, Age = (flights$Year * 12) + flights$Month - flights$acStart)
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[Big\_Data\_Example.pdf](attachments/17042692/17042690.pdf)
+(application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
+Shot 2017-03-08 at 10.19.41 AM.png](attachments/17042692/17042691.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
+Shot 2017-03-08 at 10.20.51 AM.png](attachments/17042692/17042693.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
+Shot 2017-03-08 at 10.27.19 AM.png](attachments/17042692/17042695.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
+Shot 2017-03-08 at 10.28.57 AM.png](attachments/17042692/17042696.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
+Shot 2017-03-08 at 10.30.11 AM.png](attachments/17042692/17042697.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[cluster\_small2.png](attachments/17042692/17042703.png) (image/png)
+
+Document generated by Confluence on Oct 24, 2018 14:56
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/events/unl_stat802_january_23rd_2017.md b/content/events/unl_stat802_january_23rd_2017.md
new file mode 100644
index 00000000..d2d96693
--- /dev/null
+++ b/content/events/unl_stat802_january_23rd_2017.md
@@ -0,0 +1,43 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [HCC Events](HCC-Events_332364.html)
+
+<span id="title-text"> HCC-DOCS : UNL STAT802, January 23rd, 2017 </span>
+=========================================================================
+
+Created by <span class="author"> Natasha Pavlovikj</span>, last modified
+by <span class="editor"> Carrie Brown</span> on Jan 23, 2017
+
+**Lab 1 Time:** 2 - 3:50 PM
+
+**Lab 2 Time:** 4 - 5:50 PM
+
+**Location:** UNL East Campus, Room 49, Hardin Hall
+
+[Slides](attachments/17041326/17041352.pdf)
+
+[Installation Info](attachments/17041326/17041361.pdf)
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[stat802\_anvil.pptx](attachments/17041326/17041331.pptx)
+(application/vnd.openxmlformats-officedocument.presentationml.presentation)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[stat802\_anvil.pptx](attachments/17041326/17041328.pptx)
+(application/vnd.openxmlformats-officedocument.presentationml.presentation)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[stat802\_anvil.pdf](attachments/17041326/17041352.pdf)
+(application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[stat802\_anvil.pptx](attachments/17041326/17041353.pptx)
+(application/vnd.openxmlformats-officedocument.presentationml.presentation)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[Installation.pdf](attachments/17041326/17041361.pdf)
+(application/pdf)
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/events/unl_stat_802_fall_2017.md b/content/events/unl_stat_802_fall_2017.md
new file mode 100644
index 00000000..d104d2f2
--- /dev/null
+++ b/content/events/unl_stat_802_fall_2017.md
@@ -0,0 +1,71 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [HCC Events](HCC-Events_332364.html)
+
+<span id="title-text"> HCC-DOCS : UNL STAT 802 Fall 2017 </span>
+================================================================
+
+Created by <span class="author"> Carrie Brown</span>, last modified by
+<span class="editor"> Jingchao Zhang</span> on Sep 17, 2017
+
+### Setting Up Anvil Instances for Windows SAS
+
+**Location:** Hardin Hall - Room 49
+
+**Time:** Friday, September 1, 2017 - 10:30 am
+
+[Slides](attachments/21071499/21071500.pdf)
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[stat802\_anvil.pdf](attachments/21071499/21071603.pdf)
+(application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[stat802\_anvil.pptx](attachments/21071499/21071604.pptx)
+(application/vnd.openxmlformats-officedocument.presentationml.presentation)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[stat802\_anvil.pdf](attachments/21071499/21071500.pdf)
+(application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[stat802\_anvil.pptx](attachments/21071499/21071501.pptx)
+(application/vnd.openxmlformats-officedocument.presentationml.presentation)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[2017-09-06-Anvil.pdf](attachments/21071499/21071618.pdf)
+(application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[2017-09-06-Anvil.pdf](attachments/21071499/21071629.pdf)
+(application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[WinSCP-5.11-Setup.exe](attachments/21071499/21071620.exe)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[2017-09-06-Introduction to HCC.pdf](attachments/21071499/21071621.pdf)
+(application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[KickStartFall17.pdf](attachments/21071499/21071622.pdf)
+(application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[HCC-Kickstart-Globus-2017095.pdf](attachments/21071499/21071623.pdf)
+(application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[OSG\_HCCKickstart\_20170906.pdf](attachments/21071499/21071625.pdf)
+(application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[OSG\_HCCKickstart\_20170906.pdf](attachments/21071499/21071624.pdf)
+(application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[HCC-Kickstart-Globus-2017095.pdf](attachments/21071499/21071626.pdf)
+(application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[2017-09-06-Anvil.pdf](attachments/21071499/21071630.pdf)
+(application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[2017-09-06-Anvil.pdf](attachments/21071499/21071619.pdf)
+(application/pdf)
+
+Document generated by Confluence on Oct 24, 2018 14:56
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/events/unl_stat_850_fall_2017.md b/content/events/unl_stat_850_fall_2017.md
new file mode 100644
index 00000000..41127893
--- /dev/null
+++ b/content/events/unl_stat_850_fall_2017.md
@@ -0,0 +1,42 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [HCC Events](HCC-Events_332364.html)
+
+<span id="title-text"> HCC-DOCS : UNL STAT 850 Fall 2017 </span>
+================================================================
+
+Created by <span class="author"> Natasha Pavlovikj</span>, last modified
+by <span class="editor"> Jingchao Zhang</span> on Sep 17, 2017
+
+**When: **1:00pm - 1:45pm
+
+**Location:** UNL East Campus, Keim 214
+
+[Slides](attachments/21071482/21071490.pdf)
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[stat850\_anvil.pdf](attachments/21071482/21071487.pdf)
+(application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[stat850\_anvil.pptx](attachments/21071482/21071488.pptx)
+(application/vnd.openxmlformats-officedocument.presentationml.presentation)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[stat850\_anvil.pdf](attachments/21071482/21071490.pdf)
+(application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[stat850\_anvil.pptx](attachments/21071482/21071491.pptx)
+(application/vnd.openxmlformats-officedocument.presentationml.presentation)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[anyconnect-macosx-4.2.00096-web-deploy-k9.dmg](attachments/21071482/21071492.dmg)
+(application/x-diskcopy)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[anyconnect-win-4.2.01022-web-deploy-k9.exe](attachments/21071482/21071493.exe)
+(application/octet-stream)
+
+Document generated by Confluence on Oct 24, 2018 14:56
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/events/unl_stat_850_fall_2018.md b/content/events/unl_stat_850_fall_2018.md
new file mode 100644
index 00000000..20ba983f
--- /dev/null
+++ b/content/events/unl_stat_850_fall_2018.md
@@ -0,0 +1,42 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [HCC Events](HCC-Events_332364.html)
+
+<span id="title-text"> HCC-DOCS : UNL STAT 850 Fall 2018 </span>
+================================================================
+
+Created by <span class="author"> Natasha Pavlovikj</span> on Aug 27,
+2018
+
+**When: **12:30pm - 1:45pm
+
+**Location:** UNL East Campus, Keim 214
+
+[Slides](attachments/35325069/35325093.pdf)
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[anyconnect-win-4.2.01022-web-deploy-k9.exe](attachments/35325069/35325070.exe)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[anyconnect-macosx-4.2.00096-web-deploy-k9.dmg](attachments/35325069/35325071.dmg)
+(application/x-diskcopy)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[stat850\_anvil.pptx](attachments/35325069/35325072.pptx)
+(application/vnd.openxmlformats-officedocument.presentationml.presentation)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[stat850\_anvil.pdf](attachments/35325069/35325073.pdf)
+(application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[stat850\_anvil.pdf](attachments/35325069/35325093.pdf)
+(application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[stat850\_anvil.pptx](attachments/35325069/35325094.pptx)
+(application/vnd.openxmlformats-officedocument.presentationml.presentation)
+
+Document generated by Confluence on Oct 24, 2018 14:56
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/events/unl_stat_950_fall_2017.md b/content/events/unl_stat_950_fall_2017.md
new file mode 100644
index 00000000..c1ff1b3f
--- /dev/null
+++ b/content/events/unl_stat_950_fall_2017.md
@@ -0,0 +1,29 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [HCC Events](HCC-Events_332364.html)
+
+<span id="title-text"> HCC-DOCS : UNL STAT 950 Fall 2017 </span>
+================================================================
+
+Created by <span class="author"> Jingchao Zhang</span>, last modified on
+Sep 18, 2017
+
+**Date**: 9 am. - 10:15 am 09/19/2017
+
+**Location**: Hardin Hall
+
+**PDF Slides**:
+
+[HCC-Intro](attachments/21072883/21072885.pdf)
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[2017-09-19-STAT950.pdf](attachments/21072883/21072885.pdf)
+(application/pdf)
+
+Document generated by Confluence on Oct 24, 2018 14:56
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/events/unl_stat_alpha_seminar_fall_2017.md b/content/events/unl_stat_alpha_seminar_fall_2017.md
new file mode 100644
index 00000000..1a47e703
--- /dev/null
+++ b/content/events/unl_stat_alpha_seminar_fall_2017.md
@@ -0,0 +1,39 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [HCC Events](HCC-Events_332364.html)
+
+<span id="title-text"> HCC-DOCS : UNL STAT Alpha Seminar Fall 2017 </span>
+==========================================================================
+
+Created by <span class="author"> Jingchao Zhang</span>, last modified on
+Sep 18, 2017
+
+**Date**: 11 am. 09/18/2017
+
+**Location**: Keim 264
+
+**PDF Slides**:
+
+[HCC\_Overview](attachments/21072863/21072872.pdf)
+
+[HCC\_Submit\_Jobs](attachments/21072863/21072864.pdf)
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[2017-09-18-Alpha-Seminar.pdf](attachments/21072863/21072870.pdf)
+(application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[2017-09-18-Alpha-Seminar.pdf](attachments/21072863/21072874.pdf)
+(application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[Stats2017.pdf](attachments/21072863/21072872.pdf) (application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[2017-09-18-Alpha-Seminar.pdf](attachments/21072863/21072864.pdf)
+(application/pdf)
+
+Document generated by Confluence on Oct 24, 2018 14:56
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/events/xsede_big_data.md b/content/events/xsede_big_data.md
new file mode 100644
index 00000000..c9daaad3
--- /dev/null
+++ b/content/events/xsede_big_data.md
@@ -0,0 +1,36 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [HCC Events](HCC-Events_332364.html)
+
+<span id="title-text"> HCC-DOCS : XSEDE Big Data </span>
+========================================================
+
+Created by <span class="author"> Carrie Brown</span>, last modified on
+Sep 13, 2017
+
+Morning Session: Recommender with Spark
+=======================================
+
+<span
+class="confluence-embedded-file-wrapper"><img src="assets/images/18547295/18547296.png" class="confluence-embedded-image" /></span>
+
+Afternoon Session - Deep Learning with TensorFlow
+=================================================
+
+<span
+class="confluence-embedded-file-wrapper"><img src="assets/images/18547295/18547300.png" class="confluence-embedded-image" /></span>
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2017-5-19\_11-41-42.png](attachments/18547295/18547296.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2017-5-19\_15-42-34.png](attachments/18547295/18547300.png)
+(image/png)
+
+Document generated by Confluence on Oct 24, 2018 14:56
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/events/xsede_workshop_big_data_november_2016.md b/content/events/xsede_workshop_big_data_november_2016.md
new file mode 100644
index 00000000..471ae37b
--- /dev/null
+++ b/content/events/xsede_workshop_big_data_november_2016.md
@@ -0,0 +1,42 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [HCC Events](HCC-Events_332364.html)
+
+<span id="title-text"> HCC-DOCS : XSEDE Workshop: Big Data - November 2016 </span>
+==================================================================================
+
+Created by <span class="author"> Emelie Harstad</span>, last modified by
+<span class="editor"> Adam Caprez</span> on Nov 01, 2016
+
+When: November 1st, 2016
+
+Where: Hardin Hall 901, UNL East Campus
+
+ 3310 Holdrege St., Lincoln, 68583
+
+Quick
+Link: <a href="http://go.unl.edu/xsedebigdata_nov2016" class="external-link">http://go.unl.edu/xsedebigdata_nov2016</a><a href="http://go.unl.edu/hccqiime2016" class="external-link"></a>
+
+<a href="http://hcc.unl.edu/xsede-hpc-workshop-big-data" class="external-link">Details</a><a href="https://portal.xsede.org/course-calendar/-/training-user/class/518/session/1096" class="external-link"></a>
+
+<a href="https://public.etherpad-mozilla.org/p/hccxsede" class="external-link">Etherpad</a><a href="https://portal.xsede.org/course-calendar/-/training-user/class/518/session/1096" class="external-link"></a>
+
+------------------------------------------------------------------------
+
+Materials
+---------
+
+| Agenda | |
+|--------|------------------------------------------------------------------------------------------------------------------------------------------------|
+| 10:00 | <a href="http://www.psc.edu/images/xsedetraining/BigDataNov2016/Big_Data_Welcome.pdf" class="external-link">Welcome</a> |
+| 10:25 | <a href="http://www.psc.edu/images/xsedetraining/BigDataNov2016/Intro_To_Big_Data.pdf" class="external-link">Intro to Big Data</a> |
+| 10:45 | <a href="http://www.psc.edu/images/xsedetraining/BigDataNov2016/BigData_Hadoop_110116.pdf" class="external-link">Hadoop</a> |
+| 12:00 | Lunch break |
+| 1:00 | <a href="http://www.psc.edu/images/xsedetraining/BigDataNov2016/Intro_To_Spark.pdf" class="external-link">Spark intro</a> |
+| 3:15 | <a href="http://www.psc.edu/images/xsedetraining/BigDataNov2016/A_Big_Big_Data_Platform.pdf" class="external-link">A Big Big Data Platform</a> |
+| 4:00 | Adjourn |
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/events/xsede_workshop_openacc_december_2016.md b/content/events/xsede_workshop_openacc_december_2016.md
new file mode 100644
index 00000000..1c303a93
--- /dev/null
+++ b/content/events/xsede_workshop_openacc_december_2016.md
@@ -0,0 +1,36 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [HCC Events](HCC-Events_332364.html)
+
+<span id="title-text"> HCC-DOCS : XSEDE Workshop: OpenACC - December 2016 </span>
+=================================================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified on
+Dec 05, 2016
+
+When: December 6th, 2016
+
+Where: Animal Science C210, UNL East Campus
+
+ 3940 Fair St., Lincoln, 68583
+
+Quick
+Link: <a href="http://go.unl.edu/xsedeopenacc" class="external-link">http://go.unl.edu/xsedeopenacc</a>
+
+<a href="https://hcc.unl.edu/xsede-hpc-workshop-openacc" class="external-link">Details</a>
+
+<a href="https://hcc.unl.edu/xsede-hpc-workshop-openacc" class="external-link"></a><span
+style="color: rgb(0,0,0);font-size: 20.0px;">Materials</span>
+
+<a href="https://www.psc.edu/index.php/136-users/training/2430-xsede-hpc-workshop-december-6-2016-openacc" class="external-link">Link to Agenda and Exercises</a>
+
+<a href="https://public.etherpad-mozilla.org/p/hccopenacc" class="external-link">Etherpad</a>
+
+
+
+------------------------------------------------------------------------
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/faq/_index.md b/content/faq/_index.md
new file mode 100644
index 00000000..4f6ac376
--- /dev/null
+++ b/content/faq/_index.md
@@ -0,0 +1,201 @@
++++
+title = "FAQ"
+weight = "20"
++++
+
+- [I have an account, now
+ what?](#FAQ(Freq.AskedQuestions)-Ihaveanaccount,nowwhat?)
+- [How do I change my
+ password?](#FAQ(Freq.AskedQuestions)-HowdoIchangemypassword?)
+- [I forgot my password, how can I retrieve
+ it?](#FAQ(Freq.AskedQuestions)-Iforgotmypassword,howcanIretrieveit?)
+- [I just deleted some files and didn't mean to! Can I get them
+ back?](#FAQ(Freq.AskedQuestions)-Ijustdeletedsomefilesanddidn'tmeanto!CanIgetthemback?)
+- [How do I (re)activate
+ Duo?](#FAQ(Freq.AskedQuestions)-HowdoI(re)activateDuo?)
+- [How many nodes/memory/time should I
+ request?](#FAQ(Freq.AskedQuestions)-Howmanynodes/memory/timeshouldIrequest?)
+- [I am trying to run a job but nothing
+ happens?](#FAQ(Freq.AskedQuestions)-Iamtryingtorunajobbutnothinghappens?)
+- [I keep getting the error "slurmstepd: error: Exceeded step memory
+ limit at some point." What does this mean and how do I fix
+ it?](#FAQ(Freq.AskedQuestions)-Ikeepgettingtheerror%22slurmstepd:error:Exceededstepmemorylimitatsomepoint.%22WhatdoesthismeanandhowdoIfixit?)
+- [I want to talk to a human about my problem. Can I do
+ that?](#FAQ(Freq.AskedQuestions)-Iwanttotalktoahumanaboutmyproblem.CanIdothat?)
+
+I have an account, now what?
+----------------------------
+
+Congrats on getting an HCC account! Now you need to connect to a Holland
+cluster. To do this, we use an SSH connection. SSH stands for Secure
+Shell, and it allows you to securely connect to a remote computer and
+operate it just like you would a personal machine.
+
+Depending on your operating system, you may need to install software to
+make this connection. Check out on Quick Start Guides for information on
+how to install the necessary software for your operating system
+
+- [For Mac/Linux Users](2851290.html)
+- [For Windows Users](For-Windows-Users_2851288.html)
+
+How do I change my password?
+----------------------------
+
+I forgot my password, how can I retrieve it?
+--------------------------------------------
+
+Information on how to change or retrieve your password can be found on
+the documentation page: [How to change your
+password](How-to-change-your-password_13041705.html)
+
+
+All passwords must be at least 8 characters in length and must contain
+at least one capital letter and one numeric digit. Passwords also cannot
+contain any dictionary words. If you need help picking a good password,
+consider using a (secure!) password generator such as
+<a href="https://www.random.org/passwords/" class="external-link">this one provided by Random.org</a>
+
+To preserve the security of your account, we recommend changing the
+default password you were given as soon as possible.
+
+I just deleted some files and didn't mean to! Can I get them back?
+------------------------------------------------------------------
+
+That depends. Where were the files you deleted?
+
+**If the files were in your $HOME directory (/home/group/user/):** It's
+possible.
+
+$HOME directories are backed up daily and we can restore your files as
+they were at the time of our last backup. Please note that any changes
+made to the files between when the backup was made and when you deleted
+them will not be preserved. To have these files restored, please contact
+HCC Support at
+<a href="mailto:hcc-support@unl.edu" class="external-link">hcc-support@unl.edu</a>
+as soon as possible.
+
+**If the files were in your $WORK directory (/work/group/user/):** No.
+
+Unfortunately, the $WORK directories are created as a short term place
+to hold job files. This storage was designed to be quickly and easily
+accessed by our worker nodes and as such is not conducive to backups.
+Any irreplaceable files should be backed up in a secondary location,
+such as Attic, the cloud, or on your personal machine. For more
+information on how to prevent file loss, check out [Preventing File
+Loss](Preventing-File-Loss_29065313.html).
+
+How do I (re)activate Duo?
+--------------------------
+
+**If you have not activated Duo before:**
+
+Please stop by
+<a href="http://hcc.unl.edu/location" class="external-link">our offices</a>
+along with a photo ID and we will be happy to activate it for you. If
+you are not local to Omaha or Lincoln, contact us at
+<a href="mailto:hcc-support@unl.edu" class="external-link">hcc-support@unl.edu</a>
+and we will help you activate Duo remotely.
+
+**If you have activated Duo previously but now have a different phone
+number:**
+
+Stop by our offices along with a photo ID and we can help you reactivate
+Duo and update your account with your new phone number.
+
+**If you have activated Duo previously and have the same phone number:**
+
+Email us at
+<a href="mailto:hcc-support@unl.edu" class="external-link">hcc-support@unl.edu</a>
+from the email address your account is registered under and we will send
+you a new link that you can use to activate Duo.
+
+How many nodes/memory/time should I request?
+--------------------------------------------
+
+**Short answer:** We don’t know.
+
+**Long answer:** The amount of resources required is highly dependent on
+the application you are using, the input file sizes and the parameters
+you select. Sometimes it can help to speak with someone else who has
+used the software before to see if they can give you an idea of what has
+worked for them.
+
+But ultimately, it comes down to trial and error; try different
+combinations and see what works and what doesn’t. Good practice is to
+check the output and utilization of each job you run. This will help you
+determine what parameters you will need in the future.
+
+For more information on how to determine how many resources a completed
+job used, check out the documentation on [Monitoring
+Jobs](Monitoring-Jobs_21070052.html).
+
+I am trying to run a job but nothing happens?
+---------------------------------------------
+
+Where are you trying to run the job from? You can check this by typing
+the command \`pwd\` into the terminal.
+
+**If you are running from inside your $HOME directory
+(/home/group/user/)**:
+
+Move your files to your $WORK directory (/work/group/user) and resubmit
+your job.
+
+The worker nodes on our clusters have read-only access to the files in
+$HOME directories. This means that when a job is submitted from $HOME,
+the scheduler cannot write the output and error files in the directory
+and the job is killed. It appears the job does nothing because no output
+is produced.
+
+I**f you are running from inside your $WORK directory:**
+
+Contact us at
+<a href="mailto:hcc-support@unl.edu" class="external-link">hcc-support@unl.edu</a>
+with your login, the name of the cluster you are running on, and the
+full path to your submit script and we will be happy to help solve the
+issue.
+
+I keep getting the error "slurmstepd: error: Exceeded step memory limit at some point." What does this mean and how do I fix it?
+--------------------------------------------------------------------------------------------------------------------------------
+
+This error occurs when the job you are running uses more memory than was
+requested in your submit script.
+
+If you specified --mem or --mem-per-cpu in your submit script, try
+increasing this value and resubmitting your job.
+
+If you did not specify --mem or --mem-per-cpu in your submit script,
+chances are the default amount allotted is not sufficient. Add the line
+\`\#SBATCH --mem=<memory\_amount>\` to your script with a
+reasonable amount of memory and try running it again. If you keep
+getting this error, continue to increase the requested memory amount and
+resubmit the job until it finishes successfully.
+
+For additional details on how to monitor usage on jobs, check out the
+documentation on [Monitoring Jobs](Monitoring-Jobs_21070052.html).
+
+If you continue to run into issues, please contact us at
+<a href="mailto:hcc-support@unl.edu" class="external-link">hcc-support@unl.edu</a>
+for additional assistance.
+
+I want to talk to a human about my problem. Can I do that?
+----------------------------------------------------------
+
+Of course! We have an open door policy and invite you to stop by
+<a href="http://hcc.unl.edu/location" class="external-link">either of our offices</a>
+anytime Monday through Friday between 9 am and 5 pm. One of the HCC
+staff would be happy to help you with whatever problem or question you
+have. Alternatively, you can drop one of us a line and we'll arrange a
+time to meet
+(<a href="http://hcc.unl.edu/contact-us" class="external-link">http://hcc.unl.edu/contact-us</a>).
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2017-9-28\_14-50-33.png](attachments/21073639/21073643.png)
+(image/png)
+
+Document generated by Confluence on Oct 24, 2018 14:47
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/_index.md b/content/guides/_index.md
new file mode 100644
index 00000000..e581928a
--- /dev/null
+++ b/content/guides/_index.md
@@ -0,0 +1,9 @@
++++
+title = "Guides"
+weight = "20"
++++
+
+In-depth guides to using HCC resources
+--------------------------------------
+
+{{% children description="true" %}}
diff --git a/content/guides/anvil/_index.md b/content/guides/anvil/_index.md
new file mode 100644
index 00000000..1eeaab7d
--- /dev/null
+++ b/content/guides/anvil/_index.md
@@ -0,0 +1,232 @@
++++
+title = "Anvil: HCC's Cloud"
+description = "How to use Anvil, HCC's OpenStack-based cloud resource"
+weight = "40"
++++
+
+<span id="title-text"> HCC-DOCS : Anvil: HCC's Cloud </span>
+============================================================
+
+Created by <span class="author"> Derek Weitzel</span>, last modified by
+<span class="editor"> Adam Caprez</span> on Apr 19, 2018
+
+- [Overview](#Anvil:HCC'sCloud-Overview)
+- [Cloud Terms](#Anvil:HCC'sCloud-CloudTerms)
+- [Steps for Access](#Anvil:HCC'sCloud-StepsforAccess)
+- [Backups](#Anvil:HCC'sCloud-Backups)
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-approve confluence-information-macro-icon"></span>
+
+Have your account and ready to go? Visit the Anvil OpenStack web
+interface at
+<a href="https://anvil.unl.edu/" class="external-link">https://anvil.unl.edu/</a>
+
+Overview
+--------
+
+Anvil is the Holland Computing Center's cloud computing resource, based
+on
+the <a href="https://www.openstack.org/" class="external-link">OpenStack</a>
+software. OpenStack is a free and open-source software platform for
+cloud computing. Anvil was created to address the needs of NU's
+research community that are not well served by a traditional
+batch-scheduled Linux cluster environment. Examples of use cases that
+are well suited to Anvil include:
+
+- A highly interactive environment, especially GUI applications
+- Require root-level access, such as kernel modification or
+ virtualization work
+- Alternate operating systems, such as Windows or other distributions
+ of Linux
+- Test cluster environments for various software frameworks, such as
+ <a href="http://hadoop.apache.org" class="external-link">Hadoop</a>
+ or
+ <a href="https://spark.apache.org" class="external-link">Spark</a>
+- Cluster applications that require a persistent resource, such as a
+ web or database server
+
+Using Anvil, one or more virtual machines (VMs) can be easily be created
+via a user-friendly web dashboard. Created VMs are then accessible from
+HCC clusters, or your own workstation once connected to the Anvil
+Virtual Private Network (VPN). Access is through standard means,
+typically via SSH for Linux VMs and Remote Desktop for Windows VMs.
+
+Cloud Terms
+-----------
+
+There are a few terms used within the OpenStack interface and in the
+instructions below that may be unfamiliar. The following brief
+definitions may be useful. More detailed information is available in
+the <a href="http://docs.openstack.org/user-guide/" class="external-link">OpenStack User Guide</a>.
+
+- ***Project**: *A project is the base unit of ownership in
+ OpenStack. Resources (CPUs, RAM, storage, etc.) are allocated and
+ user accounts are associated with a project. Within Anvil, each HCC
+ research group corresponds directly to a project. Similar to
+ resource allocation on HCC clusters, the members of a group share
+ the [project's resources](13599589.html).
+
+- ***Image**: * An image corresponds to everything needed to create a
+ virtual machine for a specific operating system (OS), such as Linux
+ or Windows. HCC creates and maintains [basic Windows and
+ Linux](Available-Images_13042823.html) images for convenience.
+ Users can also create their own images that can then be uploaded to
+ OpenStack and used within the project.
+
+- ***Flavor**:* A flavor (also known as *instance type*), defines the
+ parameters (i.e. resources) of the virtual machine. This includes
+ things such as number of CPUs, amount of RAM, storage, etc. There
+ are many instance types [available within
+ Anvil](Anvil-Instance-Types_13042763.html), designed to meet a
+ variety of needs.
+
+- ***Instance**:* An instance is a running virtual machine, created
+ by combining an image (the basic OS) with a flavor (resources).
+ That is, *Image + Flavor = Instance*.
+
+- ***Volume**: *A volume is a means for persistent storage within
+ OpenStack. When an instance is destroyed, any additional data that
+ was on the OS hard drive is lost. A volume can be thought of
+ similar to an external hard drive. It can be attached to an
+ instance and accessed as a second drive. When the instance is
+ destroyed, data on the volume is retained. It can then be attached
+ and accessed from another instance later.
+
+Steps for Access
+----------------
+
+The guide below outlines the steps needed to begin using Anvil. Please
+note that Anvil is currently in the *beta testing* phase. While
+reasonable precautions are taken against data loss, **sole copies of
+precious or irreproducible data should not be placed or left on Anvil**.
+
+1. **Request access to Anvil**
+ Access and resources are provided on a per-group basis, similar to
+ HCC clusters. For details, please see [What are the per group
+ resource limits?](13599589.html) To begin using Anvil, the group
+ owner should fill out the short request form
+ at <a href="http://hcc.unl.edu/request-anvil-access" class="external-link">http://hcc.unl.edu/request-anvil-access</a>.
+ An automated confirmation email will be sent, and an HCC staff
+ member will follow-up once access is available.
+ **
+ **
+2. **Create SSH keys**
+ OpenStack uses SSH key pairs to identify users and control access to
+ the VMs themselves, as opposed to the traditional username/password
+ combination. SSH key pairs consist of two files, a public key and a
+ private key. The public file can be shared freely; this file will
+ be uploaded to OpenStack and associated with your account. The
+ private key file should be treated the same as a password. **Do not
+ share your private key and always keep it in a secure location.**
+ Even if you have previously created a key pair for another purpose,
+ it's best practice to create a dedicated pair for use with Anvil.
+ The process for creating key pairs is different between Windows and
+ Mac. Follow the relevant guide below for your operating system.
+ 1. [Creating SSH key pairs on
+ Windows](Creating-SSH-key-pairs-on-Windows_13598839.html)
+ 2. [Creating SSH key pairs on Mac
+ ](Creating-SSH-key-pairs-on-Mac_13598841.html)
+
+ **
+ **
+3. **Connect to the Anvil VPN**
+ The Anvil web portal is accessible from the Internet. On the other
+ hand, for security reasons, the Anvil instances are not generally
+ accessible from the Internet. In order to access the instances from
+ on and off-campus, you will need to first be connected to the Anvil
+ VPN. Follow the instructions below to connect.
+ 1. [Connecting to the Anvil VPN
+ ](Connecting-to-the-Anvil-VPN_13042829.html)
+
+ **
+ **
+4. **Add the SSH Key Pair to your account**
+ Before creating your first instance, you'll need to associate the
+ SSH key created in step 2 with your account. Follow the guide
+ below to login to the web dashboard and add the key pair.
+ 1. [Adding SSH Key Pairs](Adding-SSH-Key-Pairs_13599025.html)**
+ **
+
+ **
+ **
+5. **Create an instance
+ **Once the setup steps above are completed, you can create an
+ instance within the web dashboard. Follow the guide below to create
+ an instance.
+ 1. [Creating an Instance](Creating-an-Instance_13599047.html)
+
+ **
+ **
+6. **Connect to your instance**
+ After an instance has been created, you can connect (login) and
+ begin to use it. Connecting is done via SSH or X2Go for Linux
+ instances and via Remote Desktop (RDP) for Windows instances.
+ Follow the relevant guide below for your instance and the type of
+ OS you're connecting from.
+ 1. [Connecting to Windows
+ Instances](Connecting-to-Windows-Instances_13042841.html)
+ 2. [Connecting to Linux Instances via SSH from
+ Mac](Connecting-to-Linux-Instances-from-Mac_13599097.html)
+ 3. [Connecting to Linux instances via SSH from
+ Windows](Connecting-to-Linux-instances-from-Windows_13599107.html)
+ 4. [Connecting to Linux instances using X2Go (for images with
+ Xfce)](Connecting-to-Linux-instances-using-X2Go_16520062.html)
+
+ **
+ **
+7. **Create and attach a volume to your instance (optional)**
+ Volumes are a means within OpenStack for persistent storage. When
+ an instance is destroyed, all data that was placed on the OS hard
+ drive is lost. A volume can be thought of similar to an external
+ hard drive. It can be attached and detached from an instance as
+ needed. Data on the volume will persist until the volume itself is
+ destroyed. Creating a volume is an optional step, but may be useful
+ in certain cases. The process of creating and attaching a volume
+ from the web dashboard is the same regardless of the type (Linux or
+ Windows) of instance it will be attached to. Once the volume is
+ attached, follow the corresponding guide for your instance's OS to
+ format and make the volume usable within your instance.
+ 1. [Creating and attaching a
+ volume](Creating-and-attaching-a-volume_13599293.html)
+ 2. [Formatting and mounting a volume in
+ Windows](Formatting-and-mounting-a-volume-in-Windows_13599295.html)
+ 3. [Formatting and mounting a volume in Linux
+ ](Formatting-and-mounting-a-volume-in-Linux_13599298.html)
+8. **Transferring files to or from your instance (optional)
+ **Transferring files to or from an instance is similar to doing so
+ with a personal laptop or workstation. To transfer between an
+ instance and another HCC resource, both SCP and [Globus
+ Connect](Globus-Connect_6357013.html) can be used. For transferring
+ between an instance and a laptop/workstation or another instance,
+ standard file sharing utilities such as Dropbox or Box can be used.
+ Globus may also be used, with one stipulation. In order to
+ transfer files between two personal endpoints, a Globus Plus
+ subscription is required. As part of HCC's Globus Provider Plan,
+ HCC can provide this on a per-user basis free of charge. If you are
+ interested in Globus Plus, please
+ email <a href="mailto:hcc-support@unl.edu" class="external-link">hcc-support@unl.edu</a> with
+ your request and a brief explanation.
+
+Backups
+-------
+
+HCC creates daily backups of images and volume snapshots for disaster
+recovery. All users' images, detached volumes, and volume snapshots will
+be backed up on a daily basis. The ephemeral disks of VMs and attached
+volumes will NOT be backed up. If you would like your attached volumes
+to be backed up, make a snapshot by going to the “Volumes” tab, click
+the down arrow next to the button “Edit Volume” of the volume you want
+to make a snapshot, then, select “Create Snapshot”.
+
+Please note the backup function is for disaster recovery use only. HCC
+is unable to restore single files within instances. Further, HCC's
+disaster recovery backups should not be the only source of backups for
+important data. The backup policies are subject to change without prior
+notice. To retrieve your backups, please contact HCC. If you have
+special concerns please
+<a href="mailto:hcc-support@unl.edu" class="external-link">contact us</a>.
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/anvil/adding_ssh_key_pairs.md b/content/guides/anvil/adding_ssh_key_pairs.md
new file mode 100644
index 00000000..d36c4037
--- /dev/null
+++ b/content/guides/anvil/adding_ssh_key_pairs.md
@@ -0,0 +1,84 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Anvil: HCC's Cloud](13042760.html)
+
+<span id="title-text"> HCC-DOCS : Adding SSH Key Pairs </span>
+==============================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified by
+<span class="editor"> Carrie Brown</span> on Sep 25, 2017
+
+If you have not already generated your key pairs and need help doing so,
+please see the documentation that relates to your operating system:
+
+- [Creating SSH key pairs on
+ Mac](Creating-SSH-key-pairs-on-Mac_13598841.html)
+- [Creating SSH key pairs on
+ Windows](Creating-SSH-key-pairs-on-Windows_13598839.html)
+
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-warning confluence-information-macro-icon"></span>
+
+This guide assumes you are either accessing Anvil from on-campus, or are
+connected to the [Anvil VPN](Connecting-to-the-Anvil-VPN_13042829.html).
+
+Log into the Anvil web dashboard
+at **<a href="https://anvil-beta.unl.edu" class="external-link">anvil-beta.unl.edu</a>** using
+your HCC credentials. On the left-hand side navigation menu,
+click *Access & Security*.
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13599025/13599031.png" class="confluence-embedded-image confluence-content-image-border" width="232" height="376" /></span>
+
+Choose the *Key Pairs* tab in the main window section.
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13599025/13599033.png" class="confluence-embedded-image confluence-content-image-border" width="432" height="109" /></span>
+
+Open your **public** key file, select the entire text, and copy it. On
+the right-hand side, click the *Import Key Pair* button.
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13599025/13599036.png" class="confluence-embedded-image confluence-content-image-border" width="909" height="146" /></span>
+
+In the pop-up window, fill in the *Key Pair Name* field with a
+convenient name. Paste the copied public key text in the larger *Public
+Key* box.
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13599025/13599039.png" class="confluence-embedded-image" width="650" /></span>
+
+Click the *Import Key Pair* button to close the pop-up and save the key.
+ You should then see an entry with the saved key (the fingerprint value
+will be different than the example below).
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13599025/13599043.png" class="confluence-embedded-image confluence-content-image-border" width="838" height="57" /></span>
+
+The key pair can now be associated with any newly created instances.
+
+
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[keypair1.png](attachments/13599025/13599032.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[keypair1.png](attachments/13599025/13599031.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[keypair2.png](attachments/13599025/13599033.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[keypair3.png](attachments/13599025/13599036.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[keypair4.png](attachments/13599025/13599041.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[keypair4.png](attachments/13599025/13599039.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[keypair5.png](attachments/13599025/13599043.png) (image/png)
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/anvil/anvil_instance_types.md b/content/guides/anvil/anvil_instance_types.md
new file mode 100644
index 00000000..c5cd654f
--- /dev/null
+++ b/content/guides/anvil/anvil_instance_types.md
@@ -0,0 +1,111 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Anvil: HCC's Cloud](13042760.html)
+
+<span id="title-text"> HCC-DOCS : Anvil Instance Types </span>
+==============================================================
+
+Created by <span class="author"> Derek Weitzel</span>, last modified by
+<span class="editor"> John Thiltges</span> on Jun 20, 2016
+
+Anvil provides many instance types that are optimized for different
+usage patterns.
+
+General Purpose Instances
+-------------------------
+
+### Use Cases
+
+Development environments, build servers, code repositories, low-traffic
+websites and web applications, micro services, early product
+experiments, small databases.
+
+<table>
+<colgroup>
+<col style="width: 25%" />
+<col style="width: 25%" />
+<col style="width: 25%" />
+<col style="width: 25%" />
+</colgroup>
+<thead>
+<tr class="header">
+<th>Instance Name</th>
+<th>CPUs</th>
+<th>Memory</th>
+<th>Root Disk</th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td>general.small</td>
+<td>1</td>
+<td>2GB </td>
+<td>20GB </td>
+</tr>
+<tr class="even">
+<td><p>general.medium</p></td>
+<td>1</td>
+<td>3.8GB </td>
+<td>40GB </td>
+</tr>
+<tr class="odd">
+<td>general.large </td>
+<td>2</td>
+<td>7.5GB</td>
+<td>80GB </td>
+</tr>
+<tr class="even">
+<td>general.xlarge</td>
+<td>4</td>
+<td>15GB</td>
+<td>160GB</td>
+</tr>
+<tr class="odd">
+<td>general.2xlarge</td>
+<td>8</td>
+<td>30GB</td>
+<td>160GB</td>
+</tr>
+<tr class="even">
+<td>general.4xlarge</td>
+<td>16</td>
+<td>60GB</td>
+<td>160GB</td>
+</tr>
+</tbody>
+</table>
+
+High-Memory Instances
+---------------------
+
+### Use Cases
+
+We recommend high memory instances for high performance databases,
+genome assembly and analysis.
+
+| Instance Name | CPUs | Memory | Root Disk |
+|----------------|------|--------|-----------|
+| memory.large | 2 | 15GB | 80GB |
+| memory.xlarge | 4 | 30GB | 160GB |
+| memory.2xlarge | 8 | 60GB | 160GB |
+| memory.4xlarge | 16 | 120GB | 160GB |
+
+Compute Instances
+-----------------
+
+### Use Cases
+
+We recommend compute instances for CPU intensive tasks which don't
+require large amounts of memory.
+
+| Instance Name | CPUs | Memory | Root Disk |
+|-----------------|------|--------|-----------|
+| compute.large | 2 | 3.8GB | 80GB |
+| compute.xlarge | 4 | 7.5GB | 160GB |
+| compute.2xlarge | 8 | 15GB | 160GB |
+| compute.4xlarge | 16 | 30GB | 160GB |
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/anvil/available_images.md b/content/guides/anvil/available_images.md
new file mode 100644
index 00000000..e70752ce
--- /dev/null
+++ b/content/guides/anvil/available_images.md
@@ -0,0 +1,186 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Anvil: HCC's Cloud](13042760.html)
+
+<span id="title-text"> HCC-DOCS : Available Images </span>
+==========================================================
+
+Created by <span class="author"> Derek Weitzel</span>, last modified by
+<span class="editor"> Adam Caprez</span> on Oct 30, 2017
+
+HCC provides pre-configured images available to researchers. Below is a
+list of available images.
+
+<table style="width:100%;">
+<colgroup>
+<col style="width: 14%" />
+<col style="width: 9%" />
+<col style="width: 10%" />
+<col style="width: 65%" />
+</colgroup>
+<thead>
+<tr class="header">
+<th>Image Name</th>
+<th>Username to Connect</th>
+<th>Access Instructions</th>
+<th>Description</th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td>Cloudera 5.12 GNOME</td>
+<td><code>cloudera</code></td>
+<td><a href="Connecting-to-Linux-instances-using-X2Go_16520062.html">X2Go instructions</a></td>
+<td>Cloudera 5.12 QuickStart VM. <strong>Note</strong>: Follow the X2Go instructions, but choose GNOME for the Session type instead of Xfce.</td>
+</tr>
+<tr class="even">
+<td>CentOS 7.4</td>
+<td><code>centos</code></td>
+<td><span>ssh -l centos <ipaddress></span></td>
+<td><span>The CentOS Linux distribution is a stable, predictable, manageable and reproducible platform derived from the sources of Red Hat Enterprise Linux (RHEL).</span></td>
+</tr>
+<tr class="odd">
+<td>CentOS 6.9</td>
+<td><code>centos</code></td>
+<td>ssh -l centos <ipaddress></td>
+<td><strong>HCC Standard OS</strong>. <span>The CentOS Linux distribution is a stable, predictable, manageable and reproducible platform derived from the sources of Red Hat Enterprise Linux (RHEL).</span></td>
+</tr>
+<tr class="even">
+<td>Fedora 26 Cloud</td>
+<td><code>fedora</code></td>
+<td>ssh -l fedora <ipaddress></td>
+<td><span style="color: rgb(34,34,34);">Fedora is a Linux distribution developed by the community-supported </span><a href="https://en.wikipedia.org/wiki/Fedora_Project" class="external-link" title="Fedora Project">Fedora Project</a><span style="color: rgb(34,34,34);"> and sponsored by the </span><a href="https://en.wikipedia.org/wiki/Red_Hat" class="external-link" title="Red Hat">Red Hat</a><span style="color: rgb(34,34,34);"> company.</span></td>
+</tr>
+<tr class="odd">
+<td>Fedora 26 Xfce</td>
+<td><code>fedora</code></td>
+<td><a href="Connecting-to-Linux-instances-using-X2Go_16520062.html">X2Go instructions</a></td>
+<td>Fedora 26 <span>with the Xfce Desktop Environment pre-installed.</span></td>
+</tr>
+<tr class="even">
+<td>Fedora 26 RStudio (Xfce)</td>
+<td><code>fedora</code></td>
+<td><a href="Connecting-to-Linux-instances-using-X2Go_16520062.html">X2Go instructions</a></td>
+<td>Fedora 26 with RStudio and <span>the Xfce Desktop Environment pre-installed.</span></td>
+</tr>
+<tr class="odd">
+<td>CentOS 7.4 Xfce</td>
+<td><code>centos</code></td>
+<td><a href="Connecting-to-Linux-instances-using-X2Go_16520062.html">X2Go instructions</a></td>
+<td><span>CentOS 7.4 with the Xfce Desktop Environment pre-installed.</span></td>
+</tr>
+<tr class="even">
+<td><span>CentOS 6.9 Xfce</span></td>
+<td><code>centos</code></td>
+<td><a href="Connecting-to-Linux-instances-using-X2Go_16520062.html">X2Go instructions</a></td>
+<td><span>CentOS 6.9 with the Xfce Desktop Environment pre-installed.</span></td>
+</tr>
+<tr class="odd">
+<td>Ubuntu 14.04 Xfce</td>
+<td><code>ubuntu</code></td>
+<td><a href="Connecting-to-Linux-instances-using-X2Go_16520062.html">X2Go instructions</a></td>
+<td><span>Ubuntu 14.04 <span>with the Xfce Desktop Environment pre-installed.</span></span></td>
+</tr>
+<tr class="even">
+<td><span>Ubuntu 16.04 Xfce</span></td>
+<td><code>ubuntu</code></td>
+<td><a href="Connecting-to-Linux-instances-using-X2Go_16520062.html">X2Go instructions</a></td>
+<td><span>Ubuntu 16.04 </span><span>with the Xfce Desktop Environment pre-installed.</span></td>
+</tr>
+<tr class="odd">
+<td><span>Ubuntu 17.04 Xfce</span></td>
+<td><code>ubuntu</code></td>
+<td><a href="Connecting-to-Linux-instances-using-X2Go_16520062.html">X2Go instructions</a></td>
+<td><span>Ubuntu 17.04 </span><span>with the Xfce Desktop Environment pre-installed.</span></td>
+</tr>
+<tr class="even">
+<td>Windows 7</td>
+<td><code>cloud-user</code></td>
+<td><a href="Connecting-to-Windows-Instances_13042841.html">Windows Instructions</a></td>
+<td>Windows 7 Enterprise edition with remote desktop access.</td>
+</tr>
+<tr class="odd">
+<td>Windows 10</td>
+<td><code>.\cloud-user</code></td>
+<td><a href="Connecting-to-Windows-Instances_13042841.html">Windows Instructions</a></td>
+<td>Windows 10 LTSB edition with remote desktop access.</td>
+</tr>
+<tr class="even">
+<td>Windows 7 Matlab</td>
+<td><code>cloud-user</code></td>
+<td><a href="Connecting-to-Windows-Instances_13042841.html">Windows Instructions</a></td>
+<td>Windows 7 Enterprise with Matlab <span>r2013b, r2014b, r2015b, r2016b, r2017a pre-installed.</span></td>
+</tr>
+<tr class="odd">
+<td>Windows 10 Matlab</td>
+<td><code>.\cloud-user</code></td>
+<td><a href="Connecting-to-Windows-Instances_13042841.html">Windows Instructions</a></td>
+<td><span>Windows 10 Enterprise with Matlab </span><span>r2013b, r2014b, r2015b, r2016b, r2017a pre-installed.</span></td>
+</tr>
+<tr class="even">
+<td>Windows 7 SAS</td>
+<td><code>cloud-user</code></td>
+<td><a href="Connecting-to-Windows-Instances_13042841.html">Windows Instructions</a></td>
+<td>Windows 7 Enterprise with SAS 9.3, 9.4 pre-installed.</td>
+</tr>
+<tr class="odd">
+<td>Windows 10 SAS</td>
+<td><code>.\cloud-user</code></td>
+<td><a href="Connecting-to-Windows-Instances_13042841.html">Windows Instructions</a></td>
+<td>Windows 10 Enterprise with SAS 9.4 pre-installed.</td>
+</tr>
+<tr class="even">
+<td>Windows 7 Mathematica</td>
+<td><code>cloud-user</code></td>
+<td><a href="Connecting-to-Windows-Instances_13042841.html">Windows Instructions</a></td>
+<td>Windows 7 Enterprise with Mathematica 10.4 and 11.0 pre-installed.</td>
+</tr>
+<tr class="odd">
+<td><span>Windows 10 Mathematica</span></td>
+<td><code>.\cloud-user</code></td>
+<td><a href="Connecting-to-Windows-Instances_13042841.html">Windows Instructions</a></td>
+<td><span>Windows 10 Enterprise with Mathematica 10.4 and 11.0 pre-installed.</span></td>
+</tr>
+<tr class="even">
+<td>Ubuntu Cloud 14.04 LTS</td>
+<td><code>ubuntu</code></td>
+<td>ssh -l ubuntu <ipaddress></td>
+<td> Ubuntu Cloud Image from the 14.04 Long Term Support release.</td>
+</tr>
+<tr class="odd">
+<td><span>Ubuntu Cloud 16.04 LTS</span></td>
+<td><code>ubuntu</code></td>
+<td><span>ssh -l ubuntu <ipaddress></span></td>
+<td><span>Ubuntu Cloud Image from the 16.04 Long Term Support release.</span></td>
+</tr>
+<tr class="even">
+<td>Ubuntu Cloud 17.04</td>
+<td><code>ubuntu</code></td>
+<td><span>ssh -l ubuntu <ipaddress></span></td>
+<td>Ubuntu Cloud Image from the 17.04 Release.</td>
+</tr>
+<tr class="odd">
+<td>Chipster 3.8.1</td>
+<td><code>ubuntu</code></td>
+<td><span>ssh -l ubuntu <ipaddress></span></td>
+<td>Pre-configured VM to run Chipster (<a href="http://chipster.csc.fi" class="external-link">http://chipster.csc.fi</a>) server.<br />
+<em>If you would like to run this VM, please contact HCC for additional setup instructions.</em> </td>
+</tr>
+<tr class="even">
+<td><p>Cloudera QuickStart VM 5.8.0-0</p></td>
+<td><code>centos</code></td>
+<td>ssh -l centos <ipaddress></td>
+<td>QuickStart VM from Cloudera with Apache Hadoop, Spark, etc. preinstalled.</td>
+</tr>
+</tbody>
+</table>
+
+
+Additional images can be produced by HCC staff by request
+at <a href="mailto:hcc-support@unl.edu" class="external-link">hcc-support@unl.edu</a>.
+
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/anvil/connecting_to_linux_instances_from_mac.md b/content/guides/anvil/connecting_to_linux_instances_from_mac.md
new file mode 100644
index 00000000..2fe0d41b
--- /dev/null
+++ b/content/guides/anvil/connecting_to_linux_instances_from_mac.md
@@ -0,0 +1,88 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Anvil: HCC's Cloud](13042760.html)
+
+<span id="title-text"> HCC-DOCS : Connecting to Linux Instances from Mac </span>
+================================================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified on
+Feb 11, 2016
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-warning confluence-information-macro-icon"></span>
+
+This guide assumes you associated your SSH Key Pair with the instance
+when it was created, and that you are connected to the [Anvil
+VPN](Connecting-to-the-Anvil-VPN_13042829.html).
+
+Access to Linux instances is via standard SSH, however SSH keys are used
+as opposed to entering a username and password.
+
+Start the built-in *Terminal* application, located in the *Utilities*
+folder under *Applications.*
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13599097/13599111.png" class="confluence-embedded-image confluence-content-image-border" width="598" height="67" /></span>
+
+Login into the web dashboard
+at <a href="https://anvil-beta.unl.edu/" class="external-link">https://anvil-beta.unl.edu</a>.
+ From the left-hand side menu, choose *Instances.*
+
+*<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13599097/13599115.png" class="confluence-embedded-image confluence-content-image-border" width="226" height="374" /></span>*
+
+This will show a table with the running instances and a few details
+about them. Take note of the *IP address* entry; this is the address
+that will be used to connect.
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13599097/13599117.png" class="confluence-embedded-image confluence-content-image-border" width="1064" height="133" /></span>
+
+In this example, the private key file is assumed to be on the desktop,
+and named `anvil_key`. Depending on which Linux OS you're using in your
+instance, the username to use will be different. See the [Available
+Images](Available-Images_13042823.html) page for a table with the
+username to use for each OS. In the *Terminal* application, run the
+command `ssh -i ~/Desktop/anvil_key centos@<ip address>`, substituting
+the IP address of your instance. For the example here, it would look
+like:
+
+<span
+class="confluence-embedded-file-wrapper"><img src="assets/images/13599097/13599205.png" class="confluence-embedded-image" /></span>
+
+The first time you connect, you will get a warning; type `yes` and hit
+Enter to continue connecting. Subsequent connections will not show this
+warning.
+
+<span
+class="confluence-embedded-file-wrapper"><img src="assets/images/13599097/13599208.png" class="confluence-embedded-image" /></span>
+
+You will now be logged into your instance and can use it.
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13599097/13599212.png" class="confluence-embedded-image" width="592" height="376" /></span>
+
+
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[mac1.png](attachments/13599097/13599111.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[connecting1.png](attachments/13599097/13599115.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[connecting2.png](attachments/13599097/13599117.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[connecting3.png](attachments/13599097/13599205.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[connecting4.png](attachments/13599097/13599209.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[connecting4.png](attachments/13599097/13599208.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[connecting5.png](attachments/13599097/13599212.png) (image/png)
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/anvil/connecting_to_linux_instances_from_windows.md b/content/guides/anvil/connecting_to_linux_instances_from_windows.md
new file mode 100644
index 00000000..f0280689
--- /dev/null
+++ b/content/guides/anvil/connecting_to_linux_instances_from_windows.md
@@ -0,0 +1,131 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Anvil: HCC's Cloud](13042760.html)
+
+<span id="title-text"> HCC-DOCS : Connecting to Linux instances from Windows </span>
+====================================================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified on
+Feb 11, 2016
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-warning confluence-information-macro-icon"></span>
+
+This guide assumes you associated your SSH Key Pair with the instance
+when it was created, and that you are connected to the [Anvil
+VPN](Connecting-to-the-Anvil-VPN_13042829.html).
+
+If do not already have the PuTTY package installed, download and install
+it
+from <a href="http://the.earth.li/~sgtatham/putty/latest/x86/putty-0.66-installer.exe" class="external-link">this link</a>.
+ Once installed, start PuTTY.
+
+Login into the web dashboard
+at <a href="https://anvil-beta.unl.edu/" class="external-link">https://anvil-beta.unl.edu</a>.
+ From the left-hand side menu, choose *Instances.*
+
+**<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13599097/13599115.png" class="confluence-embedded-image confluence-content-image-border" width="226" height="374" /></span>**
+
+This will show a table with the running instances and a few details
+about them. Take note of the *IP address* entry; this is the address
+that will be used to connect.
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13599097/13599117.png" class="confluence-embedded-image confluence-content-image-border" width="1064" height="133" /></span>
+
+In this example, the private key file is assumed to be
+named `anvil_key.ppk `and saved on the desktop. In PuTTY window, click
+the '+' icon next to *SSH *under *Connection* to expand the menu.
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13599107/13599229.png" class="confluence-embedded-image" width="450" /></span>
+
+Next, click the *Auth* menu item.
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13599107/13599231.png" class="confluence-embedded-image" width="450" /></span>
+
+Click the *Browse* button and the select the `anvil_key.ppk `file.
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13599107/13599236.png" class="confluence-embedded-image" width="450" /></span>
+
+With the private key selected, click the *Session* menu option at the
+top to return to the original PuTTY window.
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13599107/13599239.png" class="confluence-embedded-image" width="450" /></span>
+
+Fill in the *Host Name (or IP address)* field with the IP address of you
+instance. Choose a name to save the settings for your instance with and
+enter it in the *Saved Sessions* field.
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13599107/13599242.png" class="confluence-embedded-image" width="450" /></span>
+
+Click the *Save* button to save everything.
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13599107/13599246.png" class="confluence-embedded-image" width="450" /></span>
+
+Next, click *Open* to connect to your instance.
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13599107/13599248.png" class="confluence-embedded-image" width="450" /></span>
+
+Since this is the first time connecting to the instance, a warning box
+will appear. Click *Yes* to continue and save the instance's key. This
+warning box will not appear on subsequent connections.
+
+<span
+class="confluence-embedded-file-wrapper"><img src="assets/images/13599107/13599251.png" class="confluence-embedded-image" /></span>
+
+You should then see a terminal window prompting for a username.
+
+<span
+class="confluence-embedded-file-wrapper"><img src="assets/images/13599107/13599255.png" class="confluence-embedded-image" /></span>
+
+ Depending on which Linux OS you're using for your instance, the
+username will be different. See the [Available
+Images](https://hcc-docs.unl.edu/display/HCCDOC/Available+Images) page
+for a table with the username corresponding to each OS. The
+example instance here is CentOS, so the username is `centos.` Enter
+the appropriate username and hit Enter. You should then be logged in.
+
+<span
+class="confluence-embedded-file-wrapper"><img src="assets/images/13599107/13599258.png" class="confluence-embedded-image" /></span>
+
+**
+**
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[putty1.PNG](attachments/13599107/13599229.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[putty2.PNG](attachments/13599107/13599233.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[putty2.PNG](attachments/13599107/13599231.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[putty3.PNG](attachments/13599107/13599236.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[putty4.PNG](attachments/13599107/13599239.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[putty5.PNG](attachments/13599107/13599242.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[putty6.PNG](attachments/13599107/13599246.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[putty7.PNG](attachments/13599107/13599248.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[putty8.PNG](attachments/13599107/13599251.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[putty9.PNG](attachments/13599107/13599255.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[putty10.PNG](attachments/13599107/13599258.png) (image/png)
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/anvil/connecting_to_linux_instances_using_x2go.md b/content/guides/anvil/connecting_to_linux_instances_using_x2go.md
new file mode 100644
index 00000000..8cd04d94
--- /dev/null
+++ b/content/guides/anvil/connecting_to_linux_instances_using_x2go.md
@@ -0,0 +1,106 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Anvil: HCC's Cloud](13042760.html)
+
+<span id="title-text"> HCC-DOCS : Connecting to Linux instances using X2Go </span>
+==================================================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified on
+Sep 12, 2016
+
+Install X2Go Client
+-------------------
+
+- Linux
+ - On RedHat or CentOS, enable EPEL repo and install x2goclient
+ package
+ - On Fedora, install x2goclient package
+- On Windows or OSX, download and run the X2Go Client installer
+ from <a href="http://wiki.x2go.org/doku.php/download:start" class="external-link">http://wiki.x2go.org/doku.php/download:start</a> or
+ via the direct links below
+ - <a href="http://code.x2go.org/releases/X2GoClient_latest_mswin32-setup.exe" class="external-link">Windows installer direct link</a>
+ - <a href="http://code.x2go.org/releases/X2GoClient_latest_macosx.dmg" class="external-link">OS X 10.6 or higher installer direct link</a>
+ - <a href="http://code.x2go.org/releases/X2GoClient_latest_macosx_10_9.dmg" class="external-link">OS X 10.9 or higher installer direct link</a>
+
+Start an instance on Anvil
+--------------------------
+
+Start a new instance with any of the [images that include
+Xfce](Available-Images_13042823.html).
+
+Steps:
+
+1. Under Compute... Instances... click the 'Launch Instance' button
+2. Choose 'Boot from image', and select your desired image (here
+ 'CentOS 7.2 Xfce' is used)
+ <span
+ class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/16520062/16520061.png" class="confluence-embedded-image confluence-content-image-border" width="550" height="556" /></span>
+3. On the 'Access and Security' tab, ensure the 'default' security
+ group is checked. This will allow incoming SSH access.
+ <span
+ class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/16520062/16520060.png" class="confluence-embedded-image confluence-content-image-border" height="250" /></span>
+4. On the 'Networking' tab, add the 'Cluster Interface' network only
+ <span
+ class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/16520062/16520059.png" class="confluence-embedded-image confluence-content-image-border" width="550" /></span>
+5. Launch the instance
+6. On the instances page, note the IP Address of your new instance
+
+Connect with the X2Go Client
+----------------------------
+
+Create a new session with the following settings:
+
+1. Host: IP address of your instance
+2. Login: centos
+3. RSA key: Configure with the id\_rsa key pair you used to create the
+ instance
+4. Session type: XFCE
+5. Click 'OK' to save your new session
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/16520062/16520057.png" class="confluence-embedded-image confluence-content-image-border" width="550" /></span>
+
+
+
+Open the connection:
+
+1. Anvil instances are on a private network. To reach them with SSH,
+ you'll need to connect to the [Anvil
+ VPN](Connecting-to-the-Anvil-VPN_13042829.html)
+2. Click on the session in X2Go Client to open it
+3. The first time you connect, you'll be asked to confirm the SSH key
+ of the remote server.
+ <span
+ class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/16520062/16520058.png" class="confluence-embedded-image confluence-content-image-border" width="500" height="103" /></span>
+4. After a couple seconds, a desktop will open. Click 'Use default
+ config' to get a standard Xfce Linux desktop.
+ <span
+ class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/16520062/16520055.png" class="confluence-embedded-image confluence-content-image-border" width="345" height="150" /></span>
+5. You're ready to use your Xfce Linux desktop
+ <span
+ class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/16520062/16520056.png" class="confluence-embedded-image confluence-content-image-border" width="333" height="250" /></span>
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[xfce-startup.png](attachments/16520062/16520055.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[xfce.png](attachments/16520062/16520056.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[x2go.png](attachments/16520062/16520057.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[ssh.png](attachments/16520062/16520058.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[instance-3.png](attachments/16520062/16520059.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[instance-1.png](attachments/16520062/16520061.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[instance-2.png](attachments/16520062/16520074.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[instance-2.png](attachments/16520062/16520060.png) (image/png)
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/anvil/connecting_to_the_anvil_vpn.md b/content/guides/anvil/connecting_to_the_anvil_vpn.md
new file mode 100644
index 00000000..05755cbf
--- /dev/null
+++ b/content/guides/anvil/connecting_to_the_anvil_vpn.md
@@ -0,0 +1,96 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Anvil: HCC's Cloud](13042760.html)
+
+<span id="title-text"> HCC-DOCS : Connecting to the Anvil VPN </span>
+=====================================================================
+
+Created by <span class="author"> John Thiltges</span>, last modified by
+<span class="editor"> Natasha Pavlovikj</span> on Jan 20, 2017
+
+Instances running in Anvil are assigned a private IP address starting
+with "10.71". You can connect to these private IP addresses from any HCC
+cluster worker or login node.
+
+To directly access your instance from your home or office computer,
+connect to the Anvil VPN service.
+
+Installing software for your PC
+-------------------------------
+
+If you've connected to your campus VPN service, you'll already have the
+Cisco AnyConnect client installed.
+
+- UNL
+ <a href="https://vpn.unl.edu/" class="external-link">https://vpn.unl.edu/</a>
+
+- UNO
+ <a href="https://vpn.unomaha.edu/" class="external-link">https://vpn.unomaha.edu/</a>
+
+- UNK
+ <a href="https://vpn.unk.edu/" class="external-link">https://vpn.unk.edu/</a>
+
+Otherwise, we recommend the
+<a href="http://openconnect.github.io/openconnect-gui/" class="external-link">OpenConnect VPN client</a>.
+
+<span style="color: rgb(0,0,0);font-size: 20.0px;">Connecting with the
+Cisco client</span>
+
+Open the "Cisco AnyConnect Secure Mobility Client" and connect to
+**anvil-vpn.unl.edu**
+
+<span
+class="confluence-embedded-file-wrapper"><img src="assets/images/13042829/13042825.png" class="confluence-embedded-image" /></span>
+
+Login with your HCC username and password
+
+<span
+class="confluence-embedded-file-wrapper"><img src="assets/images/13042829/13042826.png" class="confluence-embedded-image" /></span>
+
+<span
+class="confluence-embedded-file-wrapper"><img src="assets/images/13042829/13042827.png" class="confluence-embedded-image" /></span>
+
+Login with Duo
+
+<span
+class="confluence-embedded-file-wrapper"><img src="assets/images/13042829/13042828.png" class="confluence-embedded-image" /></span>
+
+| Type... | To... |
+|------------|------------------------------------------------------------------------------------------|
+| ***push*** | Push a login request to your phone. Just review the request and tap "Approve" to log in. |
+| *phone* | Authenticate via phone callback. |
+| *sms* | Get a new batch of SMS passcodes. |
+| A passcode | Log in using a passcode, either generated with Duo Mobile, or your YubiKey |
+
+<span style="color: rgb(0,0,0);">Installing software for your Android or Apple device</span>
+--------------------------------------------------------------------------------------------
+
+- <span style="color: rgb(0,0,0);">Android</span>
+ - <span
+ style="color: rgb(0,0,0);">Install <a href="https://play.google.com/store/apps/details?id=app.openconnect" class="external-link">OpenConnect</a> or
+ <a href="https://play.google.com/store/apps/details?id=com.cisco.anyconnect.vpn.android.avf" class="external-link">AnyConnect ICS+</a><span
+ style="color: rgb(0,0,0);"> </span>from the Google Play
+ Store</span>
+- <span style="color: rgb(0,0,0);">Apple</span>
+ - <span style="color: rgb(0,0,0);">Install
+ <a href="https://itunes.apple.com/us/app/cisco-anyconnect/id392790924" class="external-link">Cisco AnyConnect</a>
+ from the Apple App Store</span>
+
+
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[cisco-0.png](attachments/13042829/13042825.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[cisco-1.png](attachments/13042829/13042826.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[cisco-2.png](attachments/13042829/13042827.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[cisco-3.png](attachments/13042829/13042828.png) (image/png)
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/anvil/connecting_to_windows_instances.md b/content/guides/anvil/connecting_to_windows_instances.md
new file mode 100644
index 00000000..27a1995d
--- /dev/null
+++ b/content/guides/anvil/connecting_to_windows_instances.md
@@ -0,0 +1,167 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Anvil: HCC's Cloud](13042760.html)
+
+<span id="title-text"> HCC-DOCS : Connecting to Windows Instances </span>
+=========================================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified on
+Oct 01, 2018
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-warning confluence-information-macro-icon"></span>
+
+This guide assumes you associated your SSH Key Pair with the instance
+when it was created, and that you are connected to the [Anvil
+VPN](Connecting-to-the-Anvil-VPN_13042829.html).
+
+Access to Windows instances is provided via Remote Desktop (RDP). When
+the Windows instance is created, the password is set randomly using your
+SSH Key Pair. This password can be retrieved via the Dashboard web
+interface, and then is used to login via Remote Desktop.
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-warning confluence-information-macro-icon"></span>
+
+Due to the size of the image and other factors, it may take several
+minutes for a Windows instance to complete setup and be accessible. It
+is recommended to wait **10 minutes** after the *Status* field shows
+*Active* before trying to connect.
+
+Once your instance is running, login to the Anvil web dashboard
+at <a href="https://anvil-beta.unl.edu/" class="external-link">https://anvil-beta.unl.edu</a> and
+click the *Instances* menu option on left-hand side. You should see an
+entry for your instance similar to the following:
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13042841/13042887.png" class="confluence-embedded-image" width="900" /></span>
+
+Click the down arrow next to *Create Snapshot* to open the drop-down
+menu and select *Retrieve Password*:
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13042841/13042846.png" class="confluence-embedded-image" height="400" /></span>
+
+This will open a new pop-up window where you will need to select
+your **private** SSH key file. Click the *Choose File* button to open a
+file explorer window.
+
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13042841/13042857.png" class="confluence-embedded-image" width="600" /></span>
+
+Navigate to your private key file and choose to open the file. The
+large text box should now have the contents of your private key. Click
+the *Decrypt Password* button:
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13042841/13042860.png" class="confluence-embedded-image" width="600" /></span>
+
+The randomly generate password should appear in the *Password* field.
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13042841/13042862.png" class="confluence-embedded-image" width="600" /></span>
+
+
+
+Copy and paste this password into a convenient text editor.
+
+Next, start your Remote Desktop client. If you are using Windows, you
+will already have the Windows-provided client program installed. For
+Mac users, there is a
+free <a href="https://itunes.apple.com/us/app/microsoft-remote-desktop/id714464092?mt=8" class="external-link">Microsoft client</a>
+in the app store.
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-warning confluence-information-macro-icon"></span>
+
+Older Remote Desktop clients may have problems connecting to Windows 10
+instances due to changes in the security protocols for Remote Desktop.
+Be sure to use an up-to-date client program when connecting to Windows
+10 instances.
+
+Determine the IP address of your instance by looking at the fourth
+column entry on the *Instances* page:
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13042841/13042890.png" class="confluence-embedded-image" width="900" /></span>
+
+Start your Remote Desktop client, enter the IP address in the name (or
+address) field, and click "Connect":
+
+<span
+class="confluence-embedded-file-wrapper"><img src="assets/images/13042841/13042879.png" class="confluence-embedded-image" /></span>
+
+When prompted, enter **cloud-user** for the username if connecting to a
+Windows 7 instance; **.\\cloud-user** if connecting to a Windows 10
+instance, and the previously recovered password.
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-warning confluence-information-macro-icon"></span>
+
+For Windows 7, the username used to connect is always <span
+style="color: rgb(0,0,255);">`cloud-user`</span>
+
+For Windows 10, the username used to connect is always <span
+style="color: rgb(0,0,255);">`.\cloud-user`</span>
+
+You may see a warning box about the certificate of the remote computer.
+ To avoid this warning in the future, check the box that says "Don't ask
+me again for connections to this computer".
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13042841/13042885.png" class="confluence-embedded-image" height="400" /></span>
+
+Click "Yes" to continue connecting. The Remote Desktop session should
+then start and you will be connected to your instance.
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
+Shot 2016-01-28 at 5.04.32 PM.png](attachments/13042841/13042845.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
+Shot 2016-01-28 at 5.11.01 PM.png](attachments/13042841/13042846.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
+Shot 2016-01-28 at 5.13.42 PM.png](attachments/13042841/13042850.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
+Shot 2016-01-28 at 5.14.54 PM.png](attachments/13042841/13042853.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
+Shot 2016-01-28 at 5.32.50 PM.png](attachments/13042841/13042874.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
+Shot 2016-01-28 at 5.34.24 PM.png](attachments/13042841/13042857.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
+Shot 2016-01-28 at 5.41.02 PM.png](attachments/13042841/13042861.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
+Shot 2016-01-28 at 5.41.02 PM.png](attachments/13042841/13042860.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
+Shot 2016-01-28 at 5.43.58 PM.png](attachments/13042841/13042862.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
+Shot 2016-01-28 at 5.32.50 PM.png](attachments/13042841/13042855.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[Capture.PNG](attachments/13042841/13042883.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[Capture.PNG](attachments/13042841/13042879.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[Capture2.PNG](attachments/13042841/13042885.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
+Shot 2016-01-29 at 4.18.33 PM.png](attachments/13042841/13042887.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
+Shot 2016-01-29 at 4.18.33 PM2.png](attachments/13042841/13042890.png)
+(image/png)
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/anvil/creating_an_instance.md b/content/guides/anvil/creating_an_instance.md
new file mode 100644
index 00000000..dd09d72f
--- /dev/null
+++ b/content/guides/anvil/creating_an_instance.md
@@ -0,0 +1,100 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Anvil: HCC's Cloud](13042760.html)
+
+<span id="title-text"> HCC-DOCS : Creating an Instance </span>
+==============================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified by
+<span class="editor"> Carrie Brown</span> on Jun 26, 2018
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-warning confluence-information-macro-icon"></span>
+
+This guide assumes you have already created SSH keys
+([Windows](Creating-SSH-key-pairs-on-Windows_13598839.html) \| [Mac](Creating-SSH-key-pairs-on-Mac_13598841.html))
+and [added](Adding-SSH-Key-Pairs_13599025.html) them to your account,
+and if off-campus that you are connected to the [Anvil
+VPN](Connecting-to-the-Anvil-VPN_13042829.html).
+
+To create an instance, an *Image* is combined with a *Flavor*.
+ Regardless of whether creating a Linux or Windows instance, the steps
+are the same. See the [Available
+Images](Available-Images_13042823.html) and [Anvil Instance
+Types](Anvil-Instance-Types_13042763.html) for details on which images
+and flavors are available. Unless you have a specific reason to choose
+otherwise, it's recommended to start with the smallest flavor usable
+with your instance.
+
+Login into the web dashboard at
+<a href="https://anvil.unl.edu" class="external-link">https://anvil.unl.edu</a>.
+ On the left-hand side menu, choose *Images*.
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13599047/13599060.png" class="confluence-embedded-image confluence-content-image-border" width="229" height="371" /></span>
+
+Click the *Public* button to see the list of publicly available images.
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13599047/13599064.png" class="confluence-embedded-image confluence-content-image-border" width="850" /></span>
+
+Choose whichever OS you would like and click the *Launch Instance*
+button on the right-hand side of the table. Here, CentOS 6.7 will be
+used as an example.
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13599047/13599068.png" class="confluence-embedded-image confluence-content-image-border" width="850" height="338" /></span>
+
+A pop-up box will appear with additional details about the instance.
+ First, enter a name for the instance and choose the flavor from the
+drop-down menu.
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13599047/13599073.png" class="confluence-embedded-image" width="600" /></span>
+
+Next, click the *Access & Security* tab. Make sure to select your SSH
+key pair from the drop-down menu, and check the *default* box
+under *Security Groups*.
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13599047/13599077.png" class="confluence-embedded-image confluence-content-image-border" width="600" /></span>
+
+Next, click the *Networking* tab. Click the small blue '+' icon in the
+*Cluster Interface* box to add it to the *Selected networks.*
+
+*<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13599047/13599081.png" class="confluence-embedded-image" width="600" /></span>*
+
+Finally, click the *Launch* button to start the instance.
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13599047/13599082.png" class="confluence-embedded-image" width="600" /></span>
+
+The *Instances* page will load, and there will be an entry for the newly
+created instance. It may take several minutes for the instance to
+complete the provisioning and startup process.
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[instances1.png](attachments/13599047/13599060.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[instances2.png](attachments/13599047/13599064.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[instances3.png](attachments/13599047/13599070.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[instances3.png](attachments/13599047/13599068.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[instances4.png](attachments/13599047/13599073.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[instances5.png](attachments/13599047/13599077.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[instances6.png](attachments/13599047/13599081.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[instances7.png](attachments/13599047/13599082.png) (image/png)
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/anvil/creating_and_attaching_a_volume.md b/content/guides/anvil/creating_and_attaching_a_volume.md
new file mode 100644
index 00000000..677bb910
--- /dev/null
+++ b/content/guides/anvil/creating_and_attaching_a_volume.md
@@ -0,0 +1,90 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Anvil: HCC's Cloud](13042760.html)
+
+<span id="title-text"> HCC-DOCS : Creating and attaching a volume </span>
+=========================================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified by
+<span class="editor"> Carrie Brown</span> on Jun 26, 2018
+
+Log into the Anvil web dashboard
+at **<a href="https://anvil.unl.edu/" class="external-link">https://anvil.unl.edu</a>** using
+your HCC credentials. On the left-hand side menu, click *Volumes*.
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13599293/13599301.png" class="confluence-embedded-image confluence-content-image-border" width="223" height="374" /></span>
+
+On the right-hand side of the page, click the *Create Volume* button.
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13599293/13599304.png" class="confluence-embedded-image confluence-content-image-border" width="470" height="80" /></span>
+
+In the pop-up window, enter a name for the volume and optionally a
+description. Choose a size for the volume (GB).
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13599293/13599306.png" class="confluence-embedded-image" width="650" /></span>
+
+Here, 10GB is used. Click the *Create Volume* button to close the
+pop-up window.
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13599293/13599307.png" class="confluence-embedded-image" width="650" /></span>
+
+You will be returned to the *Volumes* page and should see an entry
+similar to this.
+
+<span
+class="confluence-embedded-file-wrapper"><img src="assets/images/13599293/13599310.png" class="confluence-embedded-image" /></span>
+
+To attach the volume to an instance, click the down arrow on far right
+to open the drop-down menu, and choose *Manage Attachments*.
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13599293/13599313.png" class="confluence-embedded-image" width="169" height="248" /></span>
+
+In the pop-up window, choose the instance you want to attach the volume
+to from the drop-down.
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13599293/13599316.png" class="confluence-embedded-image" width="650" /></span>
+
+Click the *Attach Volume* button to finish and close the window.
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13599293/13599317.png" class="confluence-embedded-image" width="650" /></span>
+
+On the *Volumes* page, you should now see that your volume is attached.
+
+<span
+class="confluence-embedded-file-wrapper"><img src="assets/images/13599293/13599320.png" class="confluence-embedded-image" /></span>
+
+
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[volumes1.png](attachments/13599293/13599301.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[volumes2.png](attachments/13599293/13599304.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[volumes3.png](attachments/13599293/13599306.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[volumes4.png](attachments/13599293/13599307.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[volumes5.png](attachments/13599293/13599310.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[volumes6.png](attachments/13599293/13599313.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[volumes7.png](attachments/13599293/13599316.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[volumes8.png](attachments/13599293/13599317.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[volumes9.png](attachments/13599293/13599320.png) (image/png)
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/anvil/creating_ssh_key_pairs_on_mac.md b/content/guides/anvil/creating_ssh_key_pairs_on_mac.md
new file mode 100644
index 00000000..56867011
--- /dev/null
+++ b/content/guides/anvil/creating_ssh_key_pairs_on_mac.md
@@ -0,0 +1,66 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Anvil: HCC's Cloud](13042760.html)
+
+<span id="title-text"> HCC-DOCS : Creating SSH key pairs on Mac </span>
+=======================================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified on
+Aug 17, 2016
+
+To create SSH key pairs on Mac, the built-in *Terminal* application is
+used, which is located in the *Utilities *folder under *Applications.*
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13598841/13598866.png" class="confluence-embedded-image confluence-content-image-border" width="598" height="67" /></span>
+
+Start *Terminal* and run the
+command `ssh-keygen -f ~/Desktop/anvil_key`. This will create two key
+files on your Desktop, one public and one private, which can later be
+moved to whatever location you prefer.
+
+<span
+class="confluence-embedded-file-wrapper"><img src="assets/images/13598841/13598870.png" class="confluence-embedded-image" /></span>
+
+A prompt will appear to enter a passphrase. Press *Enter* twice to
+continue and create the key without a passphrase.
+
+<span
+class="confluence-embedded-file-wrapper"><img src="assets/images/13598841/13598876.png" class="confluence-embedded-image" /></span>
+
+<span
+class="confluence-embedded-file-wrapper"><img src="assets/images/13598841/13598877.png" class="confluence-embedded-image" /></span>
+
+The command will complete and you will see a message saying the files
+have been created.
+
+<span
+class="confluence-embedded-file-wrapper"><img src="assets/images/13598841/13598880.png" class="confluence-embedded-image" /></span>
+
+There will now be two key files on your Desktop. The public key is
+named `anvil_key.pub`. This public key will later be added to your
+Anvil account for SSH access to your instances. The private key is
+named `anvil_key `(no .pub extension). **Treat the private key file the
+same as you would a password. Keep your private key in a secure
+location and do not share it with anyone.**
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[mac1.png](attachments/13598841/13598866.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[mac2.png](attachments/13598841/13598873.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[mac2.png](attachments/13598841/13598870.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[mac3.png](attachments/13598841/13598876.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[mac4.png](attachments/13598841/13598877.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[mac5.png](attachments/13598841/13598880.png) (image/png)
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/anvil/creating_ssh_key_pairs_on_windows.md b/content/guides/anvil/creating_ssh_key_pairs_on_windows.md
new file mode 100644
index 00000000..783907d7
--- /dev/null
+++ b/content/guides/anvil/creating_ssh_key_pairs_on_windows.md
@@ -0,0 +1,99 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Anvil: HCC's Cloud](13042760.html)
+
+<span id="title-text"> HCC-DOCS : Creating SSH key pairs on Windows </span>
+===========================================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified by
+<span class="editor"> Natasha Pavlovikj</span> on Jul 28, 2017
+
+To create SSH keys on Windows, a companion program to the popular SSH
+client PuTTY will be used. Download and install the PuTTY package
+at <a href="https://the.earth.li/~sgtatham/putty/0.70/w32/putty-0.70-installer.msi" class="external-link">this link</a>.
+ This will install both PuTTY itself and the PuTTYgen program to
+generate the key pair.
+
+Once installed, start PuTTYgen. Click the *Generate* key to create the
+key pair.
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13598839/13598846.png" class="confluence-embedded-image" width="450" /></span>
+
+You will be promoted to move the mouse in a random fashion within the
+window for several seconds to create the key. Once the key is
+generated, the public and private keys need to be saved to different
+files. The public key is in the text box near the top of the PuTTYgen
+window. Right click within the box and choose *Select All*.
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13598839/13598847.png" class="confluence-embedded-image" width="450" /></span>
+
+Either right-click again and choose *Copy* or use *Ctrl-C* to copy the
+key text. Paste the key into a text editor of your choice. Save the
+file somewhere convenient, making sure to **save the key as plain text
+only. ** This public key will later be added to your Anvil account for
+SSH access to your instances.
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-warning confluence-information-macro-icon"></span>
+
+ The filename does not matter. By convention, both keys are named the
+same, with a '.pub' extension added to the public one. For example, the
+public key would be named `anvil_key.pub`, and the private key
+just `anvil_key`.
+
+The private key will actually need to be saved twice. This is because
+PuTTY uses its own PPK format for private keys, and the
+command-line `ssh` program uses the OpenSSH format. Depending on which
+program you're using to connect, you'll need to use the appropriate
+file.
+
+To save the private key for use with the `ssh `command, choose *Export
+OpenSSH key* under the *Conversions* menu.
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13598839/13598856.png" class="confluence-embedded-image" width="450" /></span>
+
+A pop-up box will appear warning about saving the key without a
+passphrase; select *Yes* to continue.
+
+<span
+class="confluence-embedded-file-wrapper"><img src="assets/images/13598839/13598859.png" class="confluence-embedded-image" /></span>
+
+Save the OpenSSH private key somewhere convenient.
+
+To save the PuTTY format file, click the *Save private key* button.
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13598839/13599219.png" class="confluence-embedded-image" width="450" /></span>
+
+An identical warning box to before will appear; click *Yes* to continue.
+
+<span
+class="confluence-embedded-file-wrapper"><img src="assets/images/13598839/13598859.png" class="confluence-embedded-image" /></span>
+
+You may need to change the filename slightly to avoid overwriting the
+OpenSSH key file. Save the `.ppk` file somewhere convenient.
+
+**Treat the private key file the same as you would a password. Keep
+your private key in a secure location and do not share it with anyone.**
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[puttygen1.PNG](attachments/13598839/13598846.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[puttygen2.PNG](attachments/13598839/13598847.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[puttygen3.PNG](attachments/13598839/13598856.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[puttygen4.PNG](attachments/13598839/13598859.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[puttygen5.PNG](attachments/13598839/13599219.png) (image/png)
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/anvil/formatting_and_mounting_a_volume_in_linux.md b/content/guides/anvil/formatting_and_mounting_a_volume_in_linux.md
new file mode 100644
index 00000000..d187f2c3
--- /dev/null
+++ b/content/guides/anvil/formatting_and_mounting_a_volume_in_linux.md
@@ -0,0 +1,168 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Anvil: HCC's Cloud](13042760.html)
+
+<span id="title-text"> HCC-DOCS : Formatting and mounting a volume in Linux </span>
+===================================================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified on
+Feb 15, 2016
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-warning confluence-information-macro-icon"></span>
+
+This guide assumes you associated your SSH Key Pair with the instance
+when it was created, and that you are connected to the [Anvil
+VPN](https://hcc-docs.unl.edu/display/HCCDOC/Connecting+to+the+Anvil+VPN).
+
+Once you have [created and
+attached](Creating-and-attaching-a-volume_13599293.html) your volume, it
+must be formatted and mounted in your Linux instance to be usable. This
+procedure is identical to what would be done when attaching a second
+hard drive to a physical machine. In this example, a 10GB volume was
+created and attached to the instance. Note that the majority of this
+guide is for a newly created volume. **If you are attaching an existing
+volume with data already on it, skip to creating a directory and
+mounting the volume.**
+
+Follow the relevant guide
+([Windows](Connecting-to-Linux-instances-from-Windows_13599107.html)
+\| [Mac](Connecting-to-Linux-Instances-from-Mac_13599097.html)) for your
+operating system to connect to your instance. Formatting and mounting
+the volume requires root privileges, so first run the
+command `sudo su -` to get a root shell.
+
+Running commands as root
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-error confluence-information-macro-icon"></span>
+
+Extreme care should be taken when running commands as `root.` It is very
+easy to permanently delete data or cause irreparable damage to your
+instance.
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13599298/13599376.png" class="confluence-embedded-image confluence-content-image-border" width="700" height="438" /></span>
+
+Next, you will need to determine what device the volume is presented as
+within Linux. Typically this will be` /dev/vdb`, but it is necessary to
+verify this to avoid mistakes, especially if you have more than one
+volume attached to an instance. The command `f``disk -l` will list the
+hard drive devices.
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13599298/13599470.png" class="confluence-embedded-image confluence-content-image-border" width="701" height="439" /></span>
+
+Here there is a completely empty (no partitions) disk device matching
+the 10GB size of the volume, so `/dev/vdb` is the correct device.
+ The `fdisk` utility will first be used to create a single partition.
+ Run the command `fdisk /dev/vdb `to start the program using the volume
+disk device.
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13599298/13599477.png" class="confluence-embedded-image confluence-content-image-border" width="702" height="439" /></span>
+
+Press `n` for new partition and hit enter.
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13599298/13599479.png" class="confluence-embedded-image confluence-content-image-border" width="699" height="439" /></span>
+
+Press `p` for primary partition and hit enter.
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13599298/13599482.png" class="confluence-embedded-image confluence-content-image-border" width="700" height="434" /></span>
+
+Enter `1` for the partition number.
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13599298/13599528.png" class="confluence-embedded-image confluence-content-image-border" width="700" height="438" /></span>
+
+At the next two prompts hit enter to accept the defaults and return to
+the main command prompt.
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13599298/13599530.png" class="confluence-embedded-image confluence-content-image-border" width="703" height="439" /></span>
+
+Finally, press `w` followed by return to save the changes and
+exit `fdisk`.
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13599298/13599533.png" class="confluence-embedded-image confluence-content-image-border" width="701" height="438" /></span>
+
+Now that a partition has been created, it can be formatted. Here, the
+EXT4 filesystem will be used. This is the default filesystem used by
+many Linux distributions including CentOS and Ubuntu, and is a good
+general choice. An alternate filesystem may be used by running a
+different format command. To format the partition using EXT4, run the
+command `mkfs.ext4 /dev/vdb1`. You will see a progress message and then
+be returned to the shell prompt.
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13599298/13599540.png" class="confluence-embedded-image confluence-content-image-border" width="702" height="439" /></span>
+
+Mounting an existing volume
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-warning confluence-information-macro-icon"></span>
+
+If you are attaching a pre-existing volume, start here.
+
+Finally, the formatted partition must be mounted as a directory to be
+used. By convention this is done under `/mnt`, but you may choose to
+mount it elsewhere depending on the usage. Here, a directory
+called `myvolume` will be created and the volume mounted there. Run the
+command `mkdir /mnt/myvolume`, followed by `mnt /dev/vdb1 /mnt/myvolume`
+to create the directory and mount the volume.
+
+<span style="font-family: monospace;"><span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13599298/13599546.png" class="confluence-embedded-image confluence-content-image-border" width="700" height="438" /></span></span>
+
+Running the command `df -h` should then show the new mounted empty
+volume.
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13599298/13599549.png" class="confluence-embedded-image confluence-content-image-border" width="705" height="440" /></span>
+
+The volume can now be used.
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[linuxvolume1.png](attachments/13599298/13599379.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[linuxvolume1.png](attachments/13599298/13599376.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[linuxvolume2.png](attachments/13599298/13599473.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[linuxvolume2.png](attachments/13599298/13599470.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
+Shot 2016-02-15 at 2.17.07 PM.png](attachments/13599298/13599476.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[linuxvolume4.png](attachments/13599298/13599477.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[linuxvolume6.png](attachments/13599298/13599481.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[linuxvolume6.png](attachments/13599298/13599479.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[linuxvolume7.png](attachments/13599298/13599482.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[linuxvolume8.png](attachments/13599298/13599528.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[linuxvolume9.png](attachments/13599298/13599530.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[linuxvolume10.png](attachments/13599298/13599533.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[linuxvolume11.png](attachments/13599298/13599539.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[linuxvolume12.png](attachments/13599298/13599540.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[linuxvolume13.png](attachments/13599298/13599546.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[linuxvolume14.png](attachments/13599298/13599549.png) (image/png)
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/anvil/formatting_and_mounting_a_volume_in_windows.md b/content/guides/anvil/formatting_and_mounting_a_volume_in_windows.md
new file mode 100644
index 00000000..935847d4
--- /dev/null
+++ b/content/guides/anvil/formatting_and_mounting_a_volume_in_windows.md
@@ -0,0 +1,137 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Anvil: HCC's Cloud](13042760.html)
+
+<span id="title-text"> HCC-DOCS : Formatting and mounting a volume in Windows </span>
+=====================================================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified on
+Feb 16, 2016
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-warning confluence-information-macro-icon"></span>
+
+This guide assumes you associated your SSH Key Pair with the instance
+when it was created, and that you are connected to the [Anvil
+VPN](https://hcc-docs.unl.edu/display/HCCDOC/Connecting+to+the+Anvil+VPN).
+
+Once you have [created and
+attached](https://hcc-docs.unl.edu/display/HCCDOC/Creating+and+attaching+a+volume) your
+volume, it must be formatted and mounted in your Windows instance to be
+usable. This procedure is identical to what would be done when
+attaching a second hard drive to a physical machine. In this example, a
+10GB volume was created and attached to the instance.
+
+Existing volumes
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-warning confluence-information-macro-icon"></span>
+
+These steps are only for a newly created volume. When attaching a
+previously formatted volume to an instance, it will automatically be
+visible as a second drive.
+
+From the *Start* menu, right-click on *Computer*, and select *Manage.*
+
+<span
+class="confluence-embedded-file-wrapper"><img src="assets/images/13599295/13599562.png" class="confluence-embedded-image" /></span>
+
+This will open the *Computer Management* utility. On the left-hand side
+menu, click *Disk Management.*
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13599295/13599566.png" class="confluence-embedded-image" width="800" /></span>
+
+You should see two entries. One for the OS hard drive, and a second
+unallocated disk.
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13599295/13599569.png" class="confluence-embedded-image" width="800" /></span>
+
+Right click anywhere in the white rectangle for the unallocated disk and
+choose *New Simple Volume...*.
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13599295/13599574.png" class="confluence-embedded-image" width="800" /></span>
+
+This will bring up the *New Simple Volume Wizard*. Click *Next *to
+continue.
+
+<span
+class="confluence-embedded-file-wrapper"><img src="assets/images/13599295/13599577.png" class="confluence-embedded-image" /></span>
+
+The default is to format the entire volume. Unless there is a specific
+reason not to, click *Next* to continue.
+
+<span
+class="confluence-embedded-file-wrapper"><img src="assets/images/13599295/13599578.png" class="confluence-embedded-image" /></span>
+
+The default is to assign the volume a drive letter (typically *D*).
+ Click *Next* to continue.
+
+<span
+class="confluence-embedded-file-wrapper"><img src="assets/images/13599295/13599579.png" class="confluence-embedded-image" /></span>
+
+Change the *Volume label* field if you wish the drive to be named
+something other than the default, and click *Next *to continue.
+
+<span
+class="confluence-embedded-file-wrapper"><img src="assets/images/13599295/13599580.png" class="confluence-embedded-image" /></span>
+
+Finally, click *Finish* to close the wizard.
+
+<span
+class="confluence-embedded-file-wrapper"><img src="assets/images/13599295/13599581.png" class="confluence-embedded-image" /></span>
+
+In the *Computer Management* window, you should now see the formatted
+and mounted volume.
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/13599295/13599584.png" class="confluence-embedded-image" width="800" /></span>
+
+If you open the *Computer* window, you should now see the volume as a
+second hard drive.
+
+<span
+class="confluence-embedded-file-wrapper"><img src="assets/images/13599295/13599585.png" class="confluence-embedded-image" /></span>
+
+The volume can now be used.
+
+
+
+
+
+
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[windowsvolume1.png](attachments/13599295/13599564.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[windowsvolume1.png](attachments/13599295/13599562.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[windowsvolume2.PNG](attachments/13599295/13599566.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[windowsvolume3.PNG](attachments/13599295/13599569.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[windowsvolume4.png](attachments/13599295/13599574.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[windowsvolume5.PNG](attachments/13599295/13599577.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[windowsvolume6.PNG](attachments/13599295/13599578.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[windowsvolume7.PNG](attachments/13599295/13599579.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[windowsvolume8.PNG](attachments/13599295/13599580.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[windowsvolume9.PNG](attachments/13599295/13599581.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[windowsvolume10.PNG](attachments/13599295/13599584.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[windowsvolume11.PNG](attachments/13599295/13599585.png) (image/png)
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/anvil/resizing_an_instance.md b/content/guides/anvil/resizing_an_instance.md
new file mode 100644
index 00000000..b6b8cef7
--- /dev/null
+++ b/content/guides/anvil/resizing_an_instance.md
@@ -0,0 +1,130 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Anvil: HCC's Cloud](13042760.html)
+
+<span id="title-text"> HCC-DOCS : Resizing an instance </span>
+==============================================================
+
+Created by <span class="author"> Zhongtao Zhang</span>, last modified by
+<span class="editor"> Carrie Brown</span> on Sep 28, 2018
+
+It is possible to resize an existing image. To do so, please follow the
+steps below.
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-info confluence-information-macro-icon"></span>
+
+An instance can only be resized to a flavor with a disk size equal or
+larger to the existing one. To use a flavor with a smaller disk size,
+you will need to create a new instance.
+
+To resize an instance:
+----------------------
+
+1. The resize procedure requires that your instance be shutdown and
+ rebooted. Ensure that your instance is ready to be shutdown. If
+ necessary, connect to your instance and stop any running
+ processes.
+
+2. Login to the Anvil Dashboard at
+ <a href="http://anvil.unl.edu" class="external-link">http://anvil.unl.edu</a>
+ with your HCC credentials.
+
+3. Click "Instances" in the menu on the left and locate your
+ instance.
+
+ <span
+ class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/35325988/35325991.png" class="confluence-embedded-image image-center" height="400" /></span>
+
+4. If you have important data in your instance and want to protect
+ against possible data loss, take a snapshot of the image.
+
+ 1. To take a snapshot, clicking the "Create Snapshot" button on the
+ right hand side of your image in the list.
+
+ <span
+ class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/35325988/35325992.png" class="confluence-embedded-image image-center" width="850" /></span>
+
+ 2. Enter an identifiable name for your snapshot and click "Create
+ Snapshot".
+
+ <span
+ class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/35325988/35325993.png" class="confluence-embedded-image image-center" height="150" /></span>
+
+ 3. You will be taken to the "Images" page, where your snapshot will
+ be Queued. Wait until the image has finished saving, as
+ indicated by the Status changing to "Active"
+
+ <span
+ class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/35325988/35326002.png" class="confluence-embedded-image image-center" width="850" /></span>
+
+ 4. Return to the Instance list by clicking "Instances" in the left
+ hand menu.
+
+5. Click the down arrow next to the "Create Snapshot" button and click
+ "Resize Instance" in the menu
+
+ <span
+ class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/35325988/35326003.png" class="confluence-embedded-image image-center" width="200" /></span>
+6. Select the desired New Flavor and click the "Resize" button.
+
+ <span
+ class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/35325988/35326004.png" class="confluence-embedded-image image-center" width="550" /></span>
+
+7. Wait until the instance is resized as indicated by the status
+ "Confirm or Revert Resize/Migrate". Click the "Confirm
+ Resize/Migrate" button to finalize the resize
+
+ <span
+ class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/35325988/35326006.png" class="confluence-embedded-image image-center" width="850" /></span>
+
+
+At this point, your instance should have a status of "Active". Connect
+to your instance and ensure that everything works as expected.
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-error confluence-information-macro-icon"></span>
+
+If your instance ends in an "Error" state or you have any issues or
+questions with resizing, please contact us at
+<a href="mailto:hcc-support@unl.edu" class="external-link">hcc-support@unl.edu</a>
+for assistance.
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2018-9-28\_11-13-33.png](attachments/35325988/35325991.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2018-9-28\_11-20-26.png](attachments/35325988/35325992.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2018-9-28\_11-22-16.png](attachments/35325988/35325993.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2018-9-28\_11-23-56.png](attachments/35325988/35325994.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2018-9-28\_11-26-56.png](attachments/35325988/35326001.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2018-9-28\_11-32-23.png](attachments/35325988/35326002.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2018-9-28\_11-34-56.png](attachments/35325988/35326003.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2018-9-28\_11-36-37.png](attachments/35325988/35326004.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2018-9-28\_11-38-41.png](attachments/35325988/35326005.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2018-9-28\_11-38-48.png](attachments/35325988/35326006.png)
+(image/png)
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/anvil/what_are_the_per_group_resource_limits.md b/content/guides/anvil/what_are_the_per_group_resource_limits.md
new file mode 100644
index 00000000..fea276b3
--- /dev/null
+++ b/content/guides/anvil/what_are_the_per_group_resource_limits.md
@@ -0,0 +1,40 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Anvil: HCC's Cloud](13042760.html)
+
+<span id="title-text"> HCC-DOCS : What are the per group resource limits? </span>
+=================================================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified by
+<span class="editor"> David Swanson</span> on Apr 23, 2018
+
+Any HCC research group may request access to Anvil by filling out
+a <a href="http://hcc.unl.edu/request-anvil-access" class="external-link">short request form</a>.
+ Initially a project (research group) will be given the following
+limits, shared amongst all users in the group.
+
+| Number of Instances | Virtual Cores | RAM | Number of Volumes | Volume Storage |
+|:-------------------:|:-------------:|:----:|:-----------------:|:--------------:|
+| 10 | 20 | 60GB | 10 | 100 GB |
+
+If the initial limits are not sufficient, the group owner may contact
+HCC, provide a brief justification (1 page or less), and request an
+increase to the following:
+
+| Number of Instances | Virtual Cores | RAM | Number of Volumes | Volume Storage |
+|:-------------------:|:-------------:|:-----:|:-----------------:|:--------------:|
+| 20 | 40 | 120GB | 20 | 200 GB |
+
+The resources above are provided at no charge. If a group requires more
+resources, that can be accommodated on a fee basis, depending on the
+amount needed. Please see the HCC
+<a href="http://hcc.unl.edu/priority-access-pricing" class="external-link">Priority Access Pricing</a>
+page for specific costs. *By default, no public IP addresses are
+provided.* Please
+contact <a href="mailto:hcc-support@unl.edu" class="external-link">hcc-support@unl.edu</a> for
+more details.
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/handling_data/_index.md b/content/guides/handling_data/_index.md
new file mode 100644
index 00000000..5dc437e9
--- /dev/null
+++ b/content/guides/handling_data/_index.md
@@ -0,0 +1,172 @@
++++
+title = "Handling Data"
+description = "How to work with and transfer data to/from HCC resources."
+weight = "30"
++++
+
+<span id="title-text"> HCC-DOCS : Handling Data </span>
+=======================================================
+
+Created by <span class="author"> Derek Weitzel</span>, last modified by
+<span class="editor"> Carrie Brown</span> on Sep 18, 2018
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-warning confluence-information-macro-icon"></span>
+
+HCC currently has no storage that is suitable for HIPAA or other PID
+data sets. Users are not permitted to store such data on HCC machines.
+
+All HCC machines have three separate areas for every user to store data,
+each intended for a different purpose. In addition, we have a transfer
+service that utilizes [Globus Connect](Globus-Connect_6357013.html).
+
+<span
+class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/332256/35325560.png" class="confluence-embedded-image image-center" width="1000" /></span>
+
+Home Directory
+--------------
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-info confluence-information-macro-icon"></span>
+
+You can access your home directory quickly using the $HOME environmental
+variable (i.e. '`cd $HOME'`).
+
+Your home directory (i.e. `/home/[group]/[username]`) is meant for items
+that take up relatively small amounts of space. For example: source
+code, program binaries, configuration files, etc. This space is
+quota-limited to **20GB per user**. The home directories are backed up
+for the purposes of best-effort disaster recovery. This space is not
+intended as an area for I/O to active jobs. **/home** is mounted
+**read-only** on cluster worker nodes to enforce this policy.
+
+Common Directory
+----------------
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-info confluence-information-macro-icon"></span>
+
+You can access your common directory quickly using the $COMMON
+environmental variable (i.e. '`cd $COMMON`')
+
+The common directory operates similarly to work and is mounted with
+**read and write capability to worker nodes all HCC Clusters**. This
+means that any files stored in common can be accessed from Crane, Tusker
+and Sandhills making this directory ideal for items that need to be
+accessed from multiple clusters such as reference databases and shared
+data files.
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-warning confluence-information-macro-icon"></span>
+
+Common is not designed for heavy I/O usage. Please continue to use your
+work directory for active job output to ensure the best performance of
+your jobs.
+
+Quotas for common are **30 TB per group**, with larger quotas available
+for purchase if needed. However, files stored here will **not be backed
+up** and are **not subject to purge** at this time. Please continue to
+backup your files to prevent irreparable data loss.
+
+Additional information on using the common directories can be found in
+the documentation on [Using the /common File System](30444241.html)
+
+High Performance Work Directory
+-------------------------------
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-info confluence-information-macro-icon"></span>
+
+You can access your work directory quickly using the $WORK environmental
+variable (i.e. '`cd $WORK'`).
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-error confluence-information-macro-icon"></span>
+
+The `/work` directories are **not backed up**. Irreparable data loss is
+possible with a mis-typed command. See [Preventing File
+Loss](Preventing-File-Loss_29065313.html) for strategies to avoid this.
+
+Every user has a corresponding directory under /work using the same
+naming convention as `/home` (i.e. `/work/[group]/[username]`). We
+encourage all users to use this space for I/O to running jobs. This
+directory can also be used when larger amounts of space are temporarily
+needed. There is a **50TB per group quota**; space in /work is shared
+among all users. It should be treated as short-term scratch space, and
+**is not backed up**. <span style="color: rgb(255,0,0);"><span
+style="color: rgb(0,0,0);">Please use the `hcc-du` command to check your
+own and your group's usage, and back up and clean up your files at
+reasonable intervals in $WORK.</span></span>
+
+### Purge Policy
+
+HCC has a **purge policy on /work** for files that become dormant.
+ After **6 months of inactivity on a file (26 weeks)**, an automated
+purge process will reclaim the used space of these dormant files. HCC
+provides the **`hcc-purge`** utility to list both the summary and the
+actual file paths of files that have been dormant for **24 weeks**.
+ This list is periodically generated; the timestamp of the last search
+is included in the default summary output when calling `hcc-purge` with
+no arguments. No output from `hcc-purge` indicates the last scan did
+not find any dormant files. `hcc-purge -l` will use the less pager to
+list the matching files for the user. The candidate list can also be
+accessed at the following path:` /lustre/purge/current/${USER}.list`.
+ This list is updated twice a week, on Mondays and Thursdays.
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-error confluence-information-macro-icon"></span>
+
+/work is intended for recent job output and not long term storage.
+Evidence of circumventing the purge policy by users will result in
+consequences including account lockout.
+
+
+
+If you have space requirements outside what is currently provided,
+please
+email <a href="mailto:hcc-support@unl.edu" class="external-link">hcc-support@unl.edu</a> and
+we will gladly discuss alternatives.
+
+[Attic](Using-Attic_11635580.html)
+----------------------------------
+
+Attic is a near line archive available for purchase at HCC. Attic
+provides reliable large data storage that is designed to be more
+reliable then `/work`, and larger than `/home`. Access to Attic is done
+through [Globus Connect](Globus-Connect_6357013.html).
+
+More details on Attic can be found on HCC's
+<a href="https://hcc.unl.edu/attic" class="external-link">Attic</a>
+website.
+
+<span style="color: rgb(0,0,0);line-height: 1.4285715;font-size: 20.0px;">[Globus Connect](Globus-Connect_6357013.html)</span>
+------------------------------------------------------------------------------------------------------------------------------
+
+For moving large amounts of data into or out of HCC resources, users are
+highly encouraged to consider using [Globus
+Connect](Globus-Connect_6357013.html).
+
+Using Box
+---------
+
+You can use your [UNL
+Box.com](Integrating-Box-with-HCC_8192521.html) account to download and
+upload files from any of the HCC clusters.
+
+
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[HCCStorageOptions\_cb\_edits.pdf](attachments/332256/30444364.pdf)
+(application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[HCCStorageOptions\_cb\_edits.png](attachments/332256/30444365.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[StorageOptions.png](attachments/332256/35325560.png) (image/png)
+
+Document generated by Confluence on Oct 24, 2018 14:54
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/handling_data/data_for_unmc_users_only.md b/content/guides/handling_data/data_for_unmc_users_only.md
new file mode 100644
index 00000000..eccdfcd6
--- /dev/null
+++ b/content/guides/handling_data/data_for_unmc_users_only.md
@@ -0,0 +1,60 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Handling Data](Handling-Data_332256.html)
+
+<span id="title-text"> HCC-DOCS : Data for UNMC users only </span>
+==================================================================
+
+Created by <span class="author"> Mako Furukawa Furukawa</span>, last
+modified on Apr 07, 2014
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-warning confluence-information-macro-icon"></span>
+
+HCC currently has no storage that is suitable for HIPAA or other PID
+data sets. Users are not permitted to store such data on HCC machines.
+
+Tusker and Crane have a special directory, only for UNMC users. Please
+note that this filesystem is still not suitable for HIPAA or other PID
+data sets.
+
+Transferring files to this machine from UNMC.
+---------------------------------------------
+
+You will need to email us
+at <a href="mailto:hcc-support@unl.edu" class="external-link">hcc-support@unl.edu</a> to
+gain access to this machine. Once you do, you can sftp to 10.14.250.1
+and upload your files. Note that sftp is your only option. You may use
+different sftp utilities depending on your platform you are logging in
+from. Email us if you need help with this. Once you are logged in, you
+should be at /volumes/UNMC1ZFS/\[group\]/\[username\], or
+/home/\[group\]/\[username\]. Both are the same location and you will be
+allowed to write files there.
+
+For Windows, learn more about logging in and uploading files
+[here](https://hcc-docs.unl.edu/display/HCCDOC/For+Windows+Users).
+
+Using your uploaded files on Tusker or Crane.
+---------------------------------------------
+
+<span style="color: rgb(51,51,51);"><span
+style="font-size: 14.0px;line-height: 1.4285715;">Using your
+uploaded </span><span
+style="font-size: 14.0px;line-height: 20.0px;">files</span><span
+style="font-size: 14.0px;line-height: 1.4285715;"> is easy. Just go to
+/shared/unmc1/\[group\]/\[username\] and your files will be in the same
+place. You may notice that the directory is not available at times. This
+is because the unmc1 directory is automounted. This means, if you try to
+go to the directory, it will show up. Just "cd" to
+/shared/unmc1/\[group\]/\[username\] and all of the files will be
+there.</span></span>
+
+If you have space requirements outside what is currently provided,
+please
+email <a href="mailto:hcc-support@unl.edu" class="external-link">hcc-support@unl.edu</a> and
+we will gladly discuss alternatives.
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/handling_data/globus_connect/_index.md b/content/guides/handling_data/globus_connect/_index.md
new file mode 100644
index 00000000..3705da5f
--- /dev/null
+++ b/content/guides/handling_data/globus_connect/_index.md
@@ -0,0 +1,181 @@
++++
+title = "Globus Connect"
++++
+<span id="title-text"> HCC-DOCS : Globus Connect </span>
+========================================================
+
+Created by <span class="author"> Emelie Harstad</span>, last modified by
+<span class="editor"> Carrie Brown</span> on Oct 27, 2017
+
+<a href="https://www.globus.org/globus-connect" class="external-link">Globus Connect</a> is
+a fast and robust file transfer service that allows users to quickly
+move large amounts of data between computer clusters and even to and
+from personal workstations. This service has been made available for
+Tusker, Crane and Sandhills, and HCC users are encouraged to use Globus
+Connect for their larger data transfers as an alternative to slower and
+more error-prone methods such as scp and winSCP.
+
+
+
+------------------------------------------------------------------------
+
+
+
+<span
+style="color: rgb(0,0,0);font-size: 16.0px;line-height: 1.5625;">Globus
+Connect Advantages</span>
+
+- Dedicated transfer servers on Tusker, Crane and Sandhills allow
+ large amounts of data to be transferred quickly between sites.
+
+- A user can install Globus Connect Personal on his or her workstation
+ to enable data transfer to and from one of the HCC sites.
+
+- Globus will notify users via email when their transfer has
+ completed.
+
+- Users can share data with other researchers who have Globus
+ accounts.
+
+- Globus' simple web interface makes data transfers and sharing easy
+ for users to initiate and manage.
+
+
+
+Getting Started
+
+Users must first sign up for an account on
+the <a href="https://www.globus.org/SignUp" class="external-link">Globus Connect website</a>.
+ Accounts are free and grant users access to any Globus endpoint for
+which they are authorized. An endpoint is simply a file system to or
+from which a user transfers files. All HCC users are authorized to
+access their own /home and /work directories on Tusker, Crane and
+Sandhills via the Globus endpoints (named: `hcc#tusker`, `hcc#crane` and
+`hcc#sandhills`). Those who have purchased Attic storage space can
+access their /attic directories via the Globus endpoint hcc\#attic. To
+initialize or activate the endpoint, users will be required to enter
+their HCC username, password, and Duo credentials for authentication.
+ The steps involved in activating endpoints and making data transfers
+are fairly straight-forward, and are described in more detail in the
+links on the right.
+
+Globus Connect CLI
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-approve confluence-information-macro-icon"></span>
+
+If you wish, you may use the [Globus Command Line
+Interface](Globus-Command-Line-Interface_21071051.html) instead of the
+web interface.
+
+**Usage Instructions**
+
+Use these links to learn more about the Globus Connect features. You
+will find detailed instructions on how to use each of the basic
+functions. Please contact us
+at <a href="mailto:hcc-support@unl.edu" class="external-link">hcc-support@unl.edu</a> if
+you encounter any difficulties.<span
+style="line-height: 1.4285715;"> </span>
+
+------------------------------------------------------------------------
+
+**<a href="https://www.globus.org/SignUp" class="external-link">Sign up for a Globus Account</a>
+(do this first!)**
+
+**[Linking Accounts for Single
+Sign-On](https://hcc-docs.unl.edu/display/HCCDOC/Linking+Accounts+for+Single+Sign-On)**
+
+**[Activating HCC
+Endpoints](https://hcc-docs.unl.edu/display/HCCDOC/Activating+HCC+Cluster+Endpoints)**
+
+**[File Transfers Between
+Endpoints](https://hcc-docs.unl.edu/display/HCCDOC/File+Transfers+Between+Endpoints)**
+
+**[File Transfers to/from Personal
+Workstations](https://hcc-docs.unl.edu/display/HCCDOC/File+Transfers+to+and+from+Personal+Workstations)**
+
+**[File Sharing](https://hcc-docs.unl.edu/display/HCCDOC/File+Sharing)**
+
+**[Creating Globus
+Groups](https://hcc-docs.unl.edu/display/HCCDOC/Creating+Globus+Groups)**
+
+<span style="line-height: 1.4285715;">
+</span>
+
+
+
+
+
+
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[endpoint\_activate.png](attachments/6357013/6750224.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[globus\_signin.png](attachments/6357013/6750225.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[manage\_endpoints.png](attachments/6357013/6750226.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[find\_endpoint.png](attachments/6357013/6750227.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[myproxy\_signin.png](attachments/6357013/6750228.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[endpoint\_activated.png](attachments/6357013/6750229.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[globus\_quick\_links.png](attachments/6357013/6750230.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[file\_transfer.png](attachments/6357013/6750231.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[transfer\_activity.png](attachments/6357013/6750232.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[personal\_endpoint.png](attachments/6357013/6750233.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[personal\_endpoint\_transfer.png](attachments/6357013/6750234.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[select\_endpoint.png](attachments/6357013/6750242.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[add\_shared\_endpoint.png](attachments/6357013/6750243.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[create\_shared\_endpoint.png](attachments/6357013/6750244.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[add\_shared\_user.png](attachments/6357013/6750245.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[successful\_add\_shared\_user.png](attachments/6357013/6750246.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[search\_for\_group.png](attachments/6357013/6750247.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[use\_selection.png](attachments/6357013/6750248.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[group\_added\_successfully.png](attachments/6357013/6750249.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[create\_new\_group.png](attachments/6357013/6750250.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[create\_group.png](attachments/6357013/6750252.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[create\_group.png](attachments/6357013/6750251.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[invite\_more\_people.png](attachments/6357013/6750253.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[send\_invitations.png](attachments/6357013/6750257.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[invitation\_awaiting\_response.tiff](attachments/6357013/6750255.tiff)
+(image/tiff)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[member\_accept.png](attachments/6357013/6750256.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[send\_invitations.png](attachments/6357013/6750254.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[awaiting\_approval.png](attachments/6357013/6750258.png) (image/png)
+
+Document generated by Confluence on Oct 24, 2018 14:54
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/handling_data/globus_connect/activating_hcc_cluster_endpoints.md b/content/guides/handling_data/globus_connect/activating_hcc_cluster_endpoints.md
new file mode 100644
index 00000000..407f9e94
--- /dev/null
+++ b/content/guides/handling_data/globus_connect/activating_hcc_cluster_endpoints.md
@@ -0,0 +1,106 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Handling Data](Handling-Data_332256.html)
+5. [Globus Connect](Globus-Connect_6357013.html)
+
+<span id="title-text"> HCC-DOCS : Activating HCC Cluster Endpoints </span>
+==========================================================================
+
+Created by <span class="author"> Emelie Harstad</span>, last modified on
+Nov 20, 2014
+
+You will not be able to transfer files to or from an HCC endpoint using
+Globus Connect without first activating the endpoint. Endpoints are
+available for Tusker (`hcc#tusker`), Crane (`hcc#crane`), Sandhills
+(`hcc#sandhills`) and Attic (`hcc#attic`). Follow the instructions
+below to activate any of these endpoints and begin making transfers.
+
+1. <a href="https://www.globus.org/SignIn" class="external-link">Sign in</a> to
+ your Globus account using your Globus username and password. (If
+ you do not have a Globus account, you must first
+ <a href="https://www.globus.org/SignUp" class="external-link">create one</a>).
+ Then click on the 'Manage Endpoints' tab in the upper right-hand
+ corner.
+ <span style="line-height: 1.4285715;">
+ </span>
+
+ <span
+ class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/6357013/6750225.png" class="confluence-embedded-image confluence-content-image-border image-center" width="600" /></span>
+
+ <span
+ class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/6357013/6750226.png" class="confluence-embedded-image confluence-content-image-border image-center" width="600" /></span>
+
+ <span style="line-height: 1.4285715;">
+ </span>
+
+2. <span style="line-height: 1.4285715;">Find the endpoint you want by
+ entering '`hcc#tusker`', '`hcc#crane`', '`hcc#sandhills`', or
+ '`hcc#attic`' in the search box and click on the 'all' tab to
+ include all endpoints. Once you have found and selected the
+ endpoint, click 'activate,' and then click on the green 'activate
+ now' button. Click 'continue'.</span>
+
+ <span style="line-height: 1.4285715;"><span
+ class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/6357013/6750227.png" class="confluence-embedded-image confluence-content-image-border image-center" width="600" /></span>
+ <span
+ class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/6357013/6750224.png" class="confluence-embedded-image confluence-content-image-border image-center" width="600" /></span></span><span
+ style="line-height: 1.4285715;">
+ </span>
+3. <span style="line-height: 1.4285715;">You will be redirected to the
+ HCC Globus Endpoint Activation page. Enter your </span>*HCC*<span
+ style="line-height: 1.4285715;"> username and password (the password
+ you usually use to log into the HCC clusters). </span>
+ <span style="line-height: 1.4285715;">
+ </span><span
+ class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/6357140/6750259.png" class="confluence-embedded-image confluence-content-image-border image-center" width="600" /></span>
+ <span style="line-height: 1.4285715;">
+ </span>
+4. <span style="line-height: 1.4285715;">Next you will be prompted to
+ provide your *Duo* credentials. If you use the Duo Mobile app on
+ your smartphone or tablet, select 'Duo Push' and then click 'Log
+ In'. Once you approve the notification that is sent to your phone,
+ the activation will be complete. If you use a Yubikey for
+ authentication, select the 'Passcode' option and then press your
+ Yubikey to complete the activation. Upon successful activation, you
+ will be redirected to your Globus *Manage Endpoints* page.</span>
+ <span style="line-height: 1.4285715;">
+ </span>
+
+ <span
+ class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/6357140/6750260.png" class="confluence-embedded-image confluence-content-image-border image-center" width="600" /></span>
+
+
+ <span
+ class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/6357013/6750229.png" class="confluence-embedded-image confluence-content-image-border image-center" width="600" /></span>
+
+
+<span style="line-height: 1.4285715;">The endpoint should now be ready
+and will not have to be activated again for the next 7 days. </span>
+To transfer files between any two HCC clusters, you will need to
+activate both endpoints. Then, click
+[here](https://hcc-docs.unl.edu/display/HCCDOC/File+Transfers+Between+Endpoints)
+for instructions on making file transfers between HCC endpoints.
+For instructions on how to make file transfers between an HCC endpoint
+and a personal computer, click
+[here](https://hcc-docs.unl.edu/display/HCCDOC/File+Transfers+to+and+from+Personal+Workstations).
+
+------------------------------------------------------------------------
+
+
+
+
+
+
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[myproxy\_signin.png](attachments/6357140/6750259.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[duo\_authentication.png](attachments/6357140/6750260.png) (image/png)
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/handling_data/globus_connect/creating_globus_groups.md b/content/guides/handling_data/globus_connect/creating_globus_groups.md
new file mode 100644
index 00000000..1a9751ee
--- /dev/null
+++ b/content/guides/handling_data/globus_connect/creating_globus_groups.md
@@ -0,0 +1,64 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Handling Data](Handling-Data_332256.html)
+5. [Globus Connect](Globus-Connect_6357013.html)
+
+<span id="title-text"> HCC-DOCS : Creating Globus Groups </span>
+================================================================
+
+Created by <span class="author"> Emelie Harstad</span>, last modified on
+Mar 27, 2014
+
+A Globus Connect group is simply a group of individual Globus users.
+ Groups are useful when you want to create a shared endpoint and give
+the same permissions to several different users. To create a group, you
+simply choose a group name and invite whomever you want to join. You
+will have complete control over the group enrollment as well as the role
+and status of each member.
+
+1. To get started, select the 'Groups' tab at the top of your Globus
+ home page. Click on 'Create New Group >>' in the bottom
+ left-hand corner of the page.
+
+ <span
+ class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/6357013/6750250.png" class="confluence-embedded-image confluence-content-image-border image-center" width="600" /></span>
+
+2. Once you have entered a unique group name and description, click
+ 'Create Group'.
+
+ <span
+ class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/6357013/6750251.png" class="confluence-embedded-image confluence-content-image-border image-center" width="600" /></span>
+
+3. To invite Globus users to join the group, select the group name from
+ the 'My Groups' tab on the left-hand side of the page. Then select
+ the 'Members' tab on the right. Click the link to 'Invite more
+ people?'.
+
+ <span
+ class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/6357013/6750253.png" class="confluence-embedded-image confluence-content-image-border image-center" width="600" /></span>
+
+4. You will be able to enter the invitee's email address directly
+ (under the 'Email' tab), or search for them using their Globus user
+ name (under the 'Search' tab). Once you have entered or selected
+ the user, click the 'Send Invitations' button.
+
+ <span
+ class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/6357013/6750254.png" class="confluence-embedded-image confluence-content-image-border image-center" width="600" /></span>
+
+5. Once the user responds to the invitation, you will still need to
+ approve their membership by selecting the 'awaiting approval'
+ message under the group's 'Home' tab. The 'Member Details' window
+ will pop up. Select the 'Role & Status' tab and click 'Accept'.
+
+ <span
+ class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/6357013/6750258.png" class="confluence-embedded-image confluence-content-image-border image-center" width="600" /></span>
+ <span
+ class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/6357013/6750256.png" class="confluence-embedded-image confluence-content-image-border image-center" width="600" /></span>
+
+
+------------------------------------------------------------------------
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/handling_data/globus_connect/file_sharing.md b/content/guides/handling_data/globus_connect/file_sharing.md
new file mode 100644
index 00000000..e0f9bf09
--- /dev/null
+++ b/content/guides/handling_data/globus_connect/file_sharing.md
@@ -0,0 +1,108 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Handling Data](Handling-Data_332256.html)
+5. [Globus Connect](Globus-Connect_6357013.html)
+
+<span id="title-text"> HCC-DOCS : File Sharing </span>
+======================================================
+
+Created by <span class="author"> Emelie Harstad</span>, last modified on
+Oct 20, 2017
+
+If you would like another colleague or researcher to have access to your
+data, you may also create a read-only shared endpoint on Tusker, Crane
+or Sandhills. You can personally manage access to this endpoint and
+give read permissions to anybody with a Globus account (whether or not
+they have an HCC account). *Please use this feature responsibly by
+sharing only what is necessary and granting access only to trusted
+users. *
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-warning confluence-information-macro-icon"></span>
+
+ Shared endpoints created in your `home` directory on HCC servers (with
+the exception of Attic) are *read-only*. You may create readable and
+writable shared endpoints in your `work` directory (or `/shared`).
+
+
+
+1. Sign in to your Globus account, click on the 'Manage Endpoints' tab
+ and search for the endpoint that you will use to host your shared
+ endpoint. For example, if you would like to share data in your
+ Tusker `work` directory, search for the `hcc#tusker` endpoint. Once
+ you have found the endpoint, it will need to be activated if it has
+ not been already (see [endpoint activation instructions
+ here](https://hcc-docs.unl.edu/display/HCCDOC/Activating+HCC+Cluster+Endpoints)).
+ If it is already activated, select the endpoint by clicking on the
+ name. Then select the 'Sharing' tab and click 'Add Shared
+ Endpoint'.
+
+ <span
+ class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/6357013/6750242.png" class="confluence-embedded-image confluence-content-image-border image-center" width="600" /></span>
+ <span
+ class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/6357013/6750243.png" class="confluence-embedded-image confluence-content-image-border image-center" width="600" /></span>
+
+2. In the 'Source Path' box, enter the full path to the directory you
+ would like to share. Only files under this directory will be shared
+ to the endpoint users you grant access. Also enter the endpoint
+ name. All shared endpoints you create will begin with your own
+ Globus userid (for example, `<userid>#tusker-share). `Provide a
+ short description of the endpoint and then click 'Create and Manage
+ Access'.
+
+
+ <span
+ class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/6357013/6750244.png" class="confluence-embedded-image confluence-content-image-border image-center" width="600" /></span>
+
+
+3. Type the Globus ID of the user to whom you would like to grant
+ access to this endpoint. Next enter the *relative path* of the
+ directory that this user should be able to access. For example, if
+ the source path of your shared endpoint
+ is `/work/<groupid>/<userid>/share` but you would like your
+ colleague to only have access
+ to `/work/<groupid>/<userid>/share/dataX`, then the 'Path' should be
+ entered as simply `/dataX. `Finally, click the blue 'Add' button.
+ You should see the message: '1 user added successfully'.
+
+ <span
+ class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/6357013/6750245.png" class="confluence-embedded-image confluence-content-image-border image-center" width="600" /></span>
+ <span
+ class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/6357013/6750246.png" class="confluence-embedded-image confluence-content-image-border image-center" width="600" /></span>
+
+
+
+4. You can also add a group of users. First you will need to create a
+ group (see [instructions for creating
+ groups](https://hcc-docs.unl.edu/display/HCCDOC/Creating+Globus+Groups)).
+ To give an entire group access to your shared endpoint, you will
+ need to search for the group name by clicking on the word
+ 'search >>' which appears just to the right of the ID text
+ box.
+
+ <span
+ class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/6357013/6750247.png" class="confluence-embedded-image confluence-content-image-border image-center" width="600" /></span>
+
+
+5. Next, enter the name of your group in the search text box, click the
+ search icon, select your group from the search results by checking
+ the box in front. Enter the relative path to which group members
+ should have access, and click the blue 'Use Selections' button at
+ the bottom. You should receive the message: 'A group added
+ successfully.'
+
+ <span
+ class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/6357013/6750248.png" class="confluence-embedded-image confluence-content-image-border image-center" width="600" /></span>
+ <span
+ class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/6357013/6750249.png" class="confluence-embedded-image confluence-content-image-border image-center" width="600" /></span>
+
+
+
+------------------------------------------------------------------------
+
+
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/handling_data/globus_connect/file_transfers_between_endpoints.md b/content/guides/handling_data/globus_connect/file_transfers_between_endpoints.md
new file mode 100644
index 00000000..4ac20bb4
--- /dev/null
+++ b/content/guides/handling_data/globus_connect/file_transfers_between_endpoints.md
@@ -0,0 +1,68 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Handling Data](Handling-Data_332256.html)
+5. [Globus Connect](Globus-Connect_6357013.html)
+
+<span id="title-text"> HCC-DOCS : File Transfers Between Endpoints </span>
+==========================================================================
+
+Created by <span class="author"> Emelie Harstad</span>, last modified by
+<span class="editor"> Adam Caprez</span> on Aug 27, 2015
+
+To transfer files between HCC clusters, you will first need to
+[activate](https://hcc-docs.unl.edu/display/HCCDOC/Activating+HCC+Cluster+Endpoints) the
+two endpoints you would like to use (the available endpoints
+are: `hcc#tusker,` `hcc#crane, hcc#sandhills`, and `hcc#attic)`. Once
+that has been completed, follow the steps below to begin transferring
+files. (Note: You can also transfer files between an HCC endpoint and
+any other Globus endpoint for which you have authorized access. That
+may include a [personal
+endpoint](https://hcc-docs.unl.edu/display/HCCDOC/File+Transfers+to+and+from+Personal+Workstations),
+a [shared
+endpoint](https://hcc-docs.unl.edu/display/HCCDOC/File+Sharing+and+Globus+Plus),
+or an endpoint on another computing resource or cluster. Once the
+endpoints have been activated, the file transfer process is generally
+the same regardless of the type of endpoints you use. For demonstration
+purposes we use two HCC endpoints.)
+
+1. Once both endpoints for the desired file transfer have been
+ activated, <a href="https://www.globus.org/SignIn" class="external-link">sign in</a> to
+ your Globus account (if you are not already) and click on the
+ 'Transfer Files' tab.
+ From <a href="http://www.globus.org" class="external-link">globus.org</a>,
+ select 'Transfer Files' from the 'Quick Links' drop-down menu.
+
+ <span
+ class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/6357013/6750230.png" class="confluence-embedded-image confluence-content-image-border image-center" width="600" /></span>
+
+2. Enter the names of the two endpoints you would like to use, or
+ select from the drop-down menus (for
+ example, `hcc#tusker` and `hcc#crane`). Click 'Go' for both
+ endpoints to view the default directory contents. Enter the
+ directory paths for both the source and destination (the 'from' and
+ 'to' paths on the respective endpoints). Click 'Go' to view files
+ under these directories. Select the files or directories you would
+ like to transfer (press *shift *or* control* to make multiple
+ selections) and click the blue highlighted arrow to start the
+ transfer.
+
+ <span
+ class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/6357013/6750231.png" class="confluence-embedded-image confluence-content-image-border image-center" width="600" /></span>
+3. The status of the transfer can be monitored from the current window
+ (scroll down to the 'Activity' heading and click the gray arrow on
+ the right-hand side of the screen). You will also receive an email
+ when your transfer has completed (or in the unlikely event that it
+ was unsuccessful).
+
+ <span
+ class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/6357013/6750232.png" class="confluence-embedded-image confluence-content-image-border image-center" width="600" /></span>
+
+
+------------------------------------------------------------------------
+
+
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/handling_data/globus_connect/file_transfers_to_and_from_personal_workstations.md b/content/guides/handling_data/globus_connect/file_transfers_to_and_from_personal_workstations.md
new file mode 100644
index 00000000..c299f1da
--- /dev/null
+++ b/content/guides/handling_data/globus_connect/file_transfers_to_and_from_personal_workstations.md
@@ -0,0 +1,68 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Handling Data](Handling-Data_332256.html)
+5. [Globus Connect](Globus-Connect_6357013.html)
+
+<span id="title-text"> HCC-DOCS : File Transfers to and from Personal Workstations </span>
+==========================================================================================
+
+Created by <span class="author"> Emelie Harstad</span>, last modified on
+Oct 19, 2016
+
+*Globus Connect Personal* allows you to transfer files to and from your
+personal computer. Once this software is installed, file transfers are
+simple and proceed in much the same way as transfers between HCC
+endpoints.
+
+1. <span
+ style="line-height: 1.4285715;">Install </span><a href="https://www.globus.org/globus-connect-personal" class="external-link">Globus Connect Personal</a><span
+ style="line-height: 1.4285715;"> on your computer. Follow the
+ detailed instructions for your operating system provided in the
+ links below:</span>
+ <span style="line-height: 1.4285715;">
+ - </span><a href="https://docs.globus.org/how-to/globus-connect-personal-mac/" class="external-link">Mac</a><a href="https://support.globus.org/entries/23879396" class="external-link"></a><span
+ style="line-height: 1.4285715;"> (Intel - OS X 10.4 or
+ higher)</span>
+ <span style="line-height: 1.4285715;">
+ - </span><a href="https://docs.globus.org/how-to/globus-connect-personal-linux/" class="external-link">Linux</a><a href="https://support.globus.org/entries/23881557" class="external-link"></a><span
+ style="line-height: 1.4285715;"> (x86-based)</span>
+ <span style="line-height: 1.4285715;">
+ - </span><a href="https://docs.globus.org/how-to/globus-connect-personal-windows/" class="external-link">Windows</a><a href="https://support.globus.org/entries/24000367" class="external-link"></a><span
+ style="line-height: 1.4285715;"> (XP, Vista, 7, 8)</span>
+ <span style="line-height: 1.4285715;">
+ </span>
+2. <span style="line-height: 1.4285715;">Once Globus Connect Personal
+ has been successfully installed, your personal endpoint will show up
+ in the 'administered by me' section of the 'Manage Endpoints' tab of
+ your Globus home page. This endpoint is private by default, and
+ therefore not visible or accessible to other Globus users.</span>
+ <span style="line-height: 1.4285715;"> </span>
+ <span style="line-height: 1.4285715;"><span
+ class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/6357013/6750233.png" class="confluence-embedded-image confluence-content-image-border image-center" width="600" /></span></span><span
+ style="line-height: 1.4285715;">
+ </span>
+3. <span style="line-height: 1.4285715;">Make transfers to and from
+ your personal endpoint just as you would from a public endpoint.
+ From your Globus account, go to the 'Transfer Files' tab and enter
+ the name of your new endpoint in one of the </span>*Endpoint*<span
+ style="line-height: 1.4285715;"> text boxes. Click 'Go' and then
+ navigate to the appropriate directory. Enter the second endpoint
+ (</span>for example: `hcc#crane,`<span
+ style="line-height: 1.4285715;"> </span>`hcc#tusker, hcc#sandhills, `or` hcc#attic`<span
+ style="line-height: 1.4285715;">), type or navigate to the desired
+ directory, and initiate the file transfer by clicking on the blue
+ arrow button.</span>
+ <span style="line-height: 1.4285715;">
+ </span><span
+ class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/6357013/6750234.png" class="confluence-embedded-image confluence-content-image-border image-center" width="600" /></span>
+
+
+
+------------------------------------------------------------------------
+
+
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/handling_data/globus_connect/globus_command_line_interface.md b/content/guides/handling_data/globus_connect/globus_command_line_interface.md
new file mode 100644
index 00000000..4bdef85f
--- /dev/null
+++ b/content/guides/handling_data/globus_connect/globus_command_line_interface.md
@@ -0,0 +1,243 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Handling Data](Handling-Data_332256.html)
+5. [Globus Connect](Globus-Connect_6357013.html)
+
+<span id="title-text"> HCC-DOCS : Globus Command Line Interface </span>
+=======================================================================
+
+Created by <span class="author"> Carrie Brown</span>, last modified on
+Jan 23, 2018
+
+Globus Command Line Interface (CLI) provides an interface to Globus
+services from the shell and can be incorporated into scripts or used
+interactively. The CLI allows users to transfer files and manipulate
+directory structures on a remote endpoint without use of the web
+interface.
+
+Connecting to Globus on the Command Line
+----------------------------------------
+
+To establish a Globus connection, a user must connect their HCC account
+to their Globus account. To do so, follow these steps:
+
+1. Connect to the desired HCC cluster.
+2. Load the Globus CLI module:
+
+ ``` syntaxhighlighter-pre
+ module load globus-cli
+ ```
+
+3. Use the command \`globus login\` to start the authorization
+ procedure. A web address will be displayed on screen. Copy and paste
+ this URL into your browser.
+
+ <span
+ class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/21071051/21071052.png" class="confluence-embedded-image image-center" height="250" /></span>
+4. If you are not already logged into Globus, do so now.
+5. Label the connection if desired, then click Allow to grant Globus
+ the permissions outlined on the screen.
+6. <span
+ class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/21071051/21071053.png" class="confluence-embedded-image image-center" width="600" /></span>Copy
+ the Authorization Code and paste it into the prompt in your
+ terminal.
+
+ **<span
+ class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/21071051/21071054.png" class="confluence-embedded-image image-center" height="400" /></span>**
+ **<span
+ class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/21071051/21071055.png" class="confluence-embedded-image image-center" height="250" /></span>**
+
+7. At this point, you can verify you are logged in:
+
+ ``` syntaxhighlighter-pre
+ globus whoami
+ ```
+
+ If you have logged in, you will see your email address displayed. If
+ not, the message "No login information available." will be
+ displayed.
+
+8. To terminate your Globus connection:
+
+ ``` syntaxhighlighter-pre
+ globus logout
+ ```
+
+Activating a Globus Endpoint
+----------------------------
+
+To find available endpoints:
+
+``` syntaxhighlighter-pre
+globus endpoint search search_term
+```
+
+Where search\_term is replaced with the keyword you wish to search for.
+For example:
+
+``` syntaxhighlighter-pre
+globus endpoint search hcc
+```
+
+will display any endpoint with "hcc" in it's Display Name.
+
+<span
+class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/21071051/21071056.png" class="confluence-embedded-image image-center" height="150" /></span>mod
+
+To use the endpoint, you can refer it it by it's UUID number. To
+activate an endpoint, use the command \`globus endpoint activate\`:
+
+<span
+class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/21071051/21073509.png" class="confluence-embedded-image image-center" width="950" /></span>
+
+Copy the given URL and paste it into the address bar of your web
+browser. If you are not already logged into the Globus website, you will
+be prompted to do so. Once you are logged in, you need to click the
+\`Activate Now\` button to activate the endpoint.
+
+<span
+class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/21071051/21073503.png" class="confluence-embedded-image image-center" height="400" /></span>
+
+Once an endpoint is activated, it will remain activate for 7 days. You
+can now transfer and manipulate files on the remote endpoint.
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-info confluence-information-macro-icon"></span>
+
+To make it easier to use, we recommend saving the UUID number as a bash
+variable to make the commands easier to use. For example, we will
+continue to use the above endpoint (Tusker) by assigning its UUID code
+to the variable \`tusker\` as follows:
+
+<span
+class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/21071051/21073499.png" class="confluence-embedded-image image-center" width="900" /></span>
+
+This command must be repeated upon each new login or terminal session
+unless you save these in your environmental variables. If you do not
+wish to do this step, you can proceed by placing the correct UUID in
+place of whenever you see \`$tusker\`.
+
+
+
+Endpoint Manipulation
+---------------------
+
+Globus CLI supports the commands \`mkdir\`, \`rename\`, and \`ls\`. All
+globus commands follow the format \`globus <command>
+<endpoint>:<file\_path>\`. We can list the files on the
+remote endpoint with the command \`globus ls\`. To list the files in the
+home directory on the remote endpoint, we would use the following
+command:
+
+<span
+class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/21071051/21073500.png" class="confluence-embedded-image image-center" width="600" /></span>
+
+To make a directory on the remote endpoint, we would use the \`globus
+mkdir\` command. For example, to make a folder in the users work
+directory on Tusker, we would use the following command:
+
+<span
+class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/21071051/21073501.png" class="confluence-embedded-image image-center" width="700" /></span>
+
+To rename files on the remote endpoint, we can use the \`globus rename\`
+command. To rename the test file we just created above, we would use the
+command:
+
+<span
+class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/21071051/21073502.png" class="confluence-embedded-image image-center" width="900" /></span>
+
+Single Item Transfers
+---------------------
+
+All transfers must take place between Globus endpoints. Even if you are
+transferring from an endpoint that you are already connected to, that
+endpoint must be activated in Globus. Here, we are transferring between
+Crane and Tusker. We have activated the Crane endpoint and saved its
+UUID to the variable $crane as we did for $tusker above.
+
+To transfer files, we use the command \`globus transfer\`. The format of
+this command is \`globus transfer <endpoint1>:<file\_path>
+<endpoint2>:<file\_path>\`. For example, here we are
+transferring the file \`testfile.txt\` from the home directory on Crane
+to the home directory on Tusker:
+
+<span
+class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/21071051/21073505.png" class="confluence-embedded-image image-center" width="900" /></span>
+
+You can then check the status of a transfer, or delete it all together,
+using the given Task ID:
+
+<span
+class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/21071051/21073506.png" class="confluence-embedded-image image-center" width="900" /></span>
+
+To transfer entire directories, simply specify a directory in the file
+path as opposed to an individual file. Below, we are transferring the
+\`output\` directory from the home directory on Crane to the home
+directory on Tusker:
+
+<span
+class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/21071051/21073507.png" class="confluence-embedded-image image-center" width="950" /></span>
+
+For additional details and information on other features of the Globus
+CLI, visit
+<a href="https://docs.globus.org/cli/examples/" class="external-link">Command Line Interface (CLI) Examples</a>
+in the Globus documentation.
+
+
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2017-8-18\_13-17-37.png](attachments/21071051/21071052.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2017-8-18\_13-21-36.png](attachments/21071051/21071053.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2017-8-18\_13-24-6.png](attachments/21071051/21071054.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2017-8-18\_13-25-34.png](attachments/21071051/21071055.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2017-8-18\_13-59-33.png](attachments/21071051/21071056.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2017-9-25\_12-41-58.png](attachments/21071051/21073498.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2017-9-25\_12-46-32.png](attachments/21071051/21073499.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2017-9-25\_12-49-24.png](attachments/21071051/21073500.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2017-9-25\_12-52-30.png](attachments/21071051/21073501.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2017-9-25\_12-54-6.png](attachments/21071051/21073502.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2017-9-25\_12-57-34.png](attachments/21071051/21073503.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2017-9-25\_13-11-46.png](attachments/21071051/21073504.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2017-9-25\_13-25-48.png](attachments/21071051/21073505.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2017-9-25\_13-26-5.png](attachments/21071051/21073506.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2017-9-25\_13-29-2.png](attachments/21071051/21073507.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2017-9-25\_13-34-30.png](attachments/21071051/21073509.png)
+(image/png)
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/handling_data/globus_connect/linking_accounts_for_single_sign_on.md b/content/guides/handling_data/globus_connect/linking_accounts_for_single_sign_on.md
new file mode 100644
index 00000000..60915ecb
--- /dev/null
+++ b/content/guides/handling_data/globus_connect/linking_accounts_for_single_sign_on.md
@@ -0,0 +1,109 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Handling Data](Handling-Data_332256.html)
+5. [Globus Connect](Globus-Connect_6357013.html)
+
+<span id="title-text"> HCC-DOCS : Linking Accounts for Single Sign-On </span>
+=============================================================================
+
+Created by <span class="author"> Emelie Harstad</span>, last modified by
+<span class="editor"> Natasha Pavlovikj</span> on Sep 07, 2015
+
+Once you've created your Globus account, you can link it to your My.UNL
+account and thereafter use your InCommon/CILogon campus credentials to
+log in to Globus (giving you one less account to keep track of).
+
+1. <span
+ style="line-height: 1.4285715;"><a href="https://www.globus.org/SignIn" class="external-link">Log in</a></span><span
+ style="line-height: 1.4285715;"> to your Globus account (or
+ <a href="https://www.globus.org/SignUp" class="external-link">create one</a></span><span
+ style="line-height: 1.4285715;"> first, if you haven't).</span>
+2. <span style="line-height: 1.4285715;">Select 'Manage Identities'
+ from the pull-down menu under your user name. </span>
+ <span style="line-height: 1.4285715;">
+ </span><span
+ class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/11633123/11633056.png" class="confluence-embedded-image confluence-content-image-border" width="650" /></span>
+ <span style="line-height: 1.4285715;">
+ </span>
+3. <span style="line-height: 1.4285715;">Click on '+ add linked
+ identity' → 'Add Single Sign-On Identity', and select 'InCommon /
+ CILogon' from the list of options. </span><span
+ style="line-height: 1.4285715;">Click 'Proceed'. </span>
+ <span style="line-height: 1.4285715;">On the next screen, select
+ 'University of Nebraska-Lincoln' as the identity provider, and then
+ select 'Log On'. </span>
+
+ <span style="line-height: 1.4285715;"><span
+ class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/11633123/11633097.png" class="confluence-embedded-image confluence-content-image-border" width="650" /></span></span>
+ <span style="line-height: 1.4285715;"><span
+ style="line-height: 1.4285715;">
+ </span></span>
+4. <span style="line-height: 1.4285715;"><span
+ style="line-height: 1.4285715;">You will be redirected to a My.UNL
+ login page. Enter your NU campus credentials and click 'LOG
+ IN'.</span></span>
+ <span style="line-height: 1.4285715;"><span
+ style="line-height: 1.4285715;">
+ </span></span><span style="line-height: 1.4285715;"><span
+ style="line-height: 1.4285715;"><span
+ class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/11633123/11633098.png" class="confluence-embedded-image confluence-content-image-border" width="650" /></span></span></span>
+ <span style="line-height: 1.4285715;"><span
+ style="line-height: 1.4285715;"><span
+ style="line-height: 1.4285715;">
+ </span></span></span>
+5. <span style="line-height: 1.4285715;"><span
+ style="line-height: 1.4285715;"><span
+ style="line-height: 1.4285715;">Finally, you will be directed back
+ to your Globus account home page, and you should see the message
+ that '*Your Globus account has been successfully linked to your
+ InCommon / CILogon account and can now be used*'.</span>
+ </span></span>
+
+
+
+From now on you can log in to Globus with just your NU campus
+credentials. To log in, do the following:
+
+1. <span style="line-height: 1.4285715;">Go to the Globus
+ <a href="https://www.globus.org/signin" class="external-link">sign in page</a></span><span
+ style="line-height: 1.4285715;">.</span>
+2. <span style="line-height: 1.4285715;">If 'InCommon / CILogon' is not
+ already chosen as the default identity provider, select it from the
+ list of options under the 'alternate login' link. </span>
+
+ <span style="line-height: 1.4285715;"><span
+ class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/11633123/11633122.png" class="confluence-embedded-image confluence-content-image-border" width="650" /></span></span>
+ <span style="line-height: 1.4285715;"><span
+ style="line-height: 1.4285715;">
+ </span></span><span style="line-height: 1.4285715;"><span
+ style="line-height: 1.4285715;">Then click 'Proceed' and select the
+ University of Nebraska-Lincoln from the list of institutions. Then
+ click 'Log On'.</span></span>
+3. <span style="line-height: 1.4285715;">You will be redirected to the
+ My.UNL login page. Enter your NU campus credentials and then 'LOG
+ IN'. (You might instead be directed to your Globus account -
+ essentially skipping this step - if you have recently entered your
+ campus credentials to log on to Globus). </span>
+
+
+
+
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[GlobusManageIdentities.png](attachments/11633123/11633056.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[GlobusSelectNU.png](attachments/11633123/11633097.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[GlobusNULogin.png](attachments/11633123/11633098.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[GlobusSelectInCommon.png](attachments/11633123/11633122.png)
+(image/png)
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/handling_data/high_speed_data_transfers.md b/content/guides/handling_data/high_speed_data_transfers.md
new file mode 100644
index 00000000..4b8f6f68
--- /dev/null
+++ b/content/guides/handling_data/high_speed_data_transfers.md
@@ -0,0 +1,48 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Handling Data](Handling-Data_332256.html)
+
+<span id="title-text"> HCC-DOCS : High-Speed Data Transfers </span>
+===================================================================
+
+Created by <span class="author"> Emelie Harstad</span>, last modified by
+<span class="editor"> Josh Samuelson</span> on May 17, 2018
+
+Tusker, Crane and Sandhills each have a dedicated transfer server with
+10 Gb/s connectivity (Sandhills currently limited to 1 Gb/s) that allows
+for faster data transfers than the login nodes. With [Globus
+Connect](https://hcc-docs.unl.edu/display/HCCDOC/Globus+Connect), users
+can take advantage of this connection speed when making large/cumbersome
+transfers.
+
+<span style="line-height: 1.4285715;">
+</span>
+
+<span style="line-height: 1.4285715;">Those who prefer scp, sftp or
+rsync clients can also benefit from this high-speed connectivity by
+using these dedicated servers for data transfers:</span>
+
+For Tusker transfers, use:
+
+For Crane transfers, use:
+
+For Sandhills Transfers, use:
+
+`tusker-xfer.unl.edu`
+
+`crane-xfer.unl.edu`
+
+`sandhills-xfer.unl.edu`
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-warning confluence-information-macro-icon"></span>
+
+Because the transfer servers are login-disabled, third-party transfers
+between `tusker-xfer,` `crane-xfer` and `sandhills-xfer` must be done
+via [Globus
+Connect](https://hcc-docs.unl.edu/display/HCCDOC/Globus+Connect).
+
+Document generated by Confluence on Oct 24, 2018 14:54
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/handling_data/integrating_box_with_hcc.md b/content/guides/handling_data/integrating_box_with_hcc.md
new file mode 100644
index 00000000..c543285f
--- /dev/null
+++ b/content/guides/handling_data/integrating_box_with_hcc.md
@@ -0,0 +1,239 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Handling Data](Handling-Data_332256.html)
+
+<span id="title-text"> HCC-DOCS : Integrating Box with HCC </span>
+==================================================================
+
+Created by <span class="author"> Derek Weitzel</span>, last modified by
+<span class="editor"> Adam Caprez</span> on Oct 11, 2018
+
+UNL has come to an arrangement
+with <a href="https://www.box.com/" class="external-link">Box.com</a> to
+provide unlimited cloud storage to every student, staff, and faculty
+member. This can be useful when used with jobs to automatically upload
+results when the job has completed. Combined with
+<a href="https://sites.box.com/sync4/" class="external-link">Box Sync</a>,
+the uploaded files can be sync'd to your laptop or desktop upon job
+completion. The upload and download speed of Box is about 20 to 30 MB/s
+in good network traffic conditions. There are two programs that can be
+used to transfer files to/from Box - `cadaver` or `lftp`. Instructions
+are provided for both options
+
+Step-by-step guide for Lftp
+---------------------------
+
+1. Create an external password for Box as described in steps 1 and 2
+ in the Cadaver instructions below.
+2. Load the `lftp` module:
+
+ **Load the lftp module**
+
+ ``` syntaxhighlighter-pre
+ module load lftp
+ ```
+
+3. Connect to Box using your full email as the username and external
+ password you created:
+
+ **Connect to Box**
+
+ ``` syntaxhighlighter-pre
+ lftp -u <username>,<password> ftps://ftp.box.com
+ ```
+
+4. Test the connection by running the `ls` command. You should see a
+ listing of your Box files. Assuming it works, add a bookmark named
+ "box" to use when connecting later:
+
+ **Add lftp bookmark**
+
+ ``` syntaxhighlighter-pre
+ lftp demo2@unl.edu@ftp.box.com:/> bookmark add box
+ ```
+
+5. Exit `lftp` by typing `quit`. To reconnect later, use bookmark
+ name:
+
+ **Connect using bookmark name**
+
+ ``` syntaxhighlighter-pre
+ lftp box
+ ```
+
+6. To upload or download files, use the `get` and `put` commands. For
+ example:
+
+ **Transferring files**
+
+ ``` syntaxhighlighter-pre
+ [demo@login.crane ~]$ lftp box
+ lftp demo2@unl.edu@ftp.box.com:/> put myfile.txt
+ lftp demo2@unl.edu@ftp.box.com:/> get my_other_file.txt
+ ```
+
+7. To download directories, use the `mirror` command. To upload
+ directories, use the `mirror` command with the `-R` option. For
+ example, to download a directory named `my_box_dir` to your current
+ directory:
+
+ **Download a directory from Box**
+
+ ``` syntaxhighlighter-pre
+ [demo@login.crane ~]$ lftp box
+ lftp demo2@unl.edu@ftp.box.com:/> mirror my_box_dir
+ ```
+
+ To upload a directory named `my_hcc_dir` to Box, use `mirror` with
+ the `-R` option:
+
+ **Upload a directory to Box**
+
+ ``` syntaxhighlighter-pre
+ [demo@login.crane ~]$ lftp box
+ lftp demo2@unl.edu@ftp.box.com:/> mirror -R my_hcc_dir
+ ```
+
+8. Lftp also supports using scripts to transfer files. This can be
+ used to automatic downloading or uploading files during jobs. <span
+ style="color: rgb(0,0,0);">For example, create a file called
+ "transfer.sh" with the following lines:</span>
+
+ **transfer.sh**
+
+ ``` syntaxhighlighter-pre
+ open box
+ get some_input_file.tar.gz
+ put my_output_file.tar.gz
+ ```
+
+ To run this script, do:
+
+ **Run transfer.sh**
+
+ ``` syntaxhighlighter-pre
+ module load lftp
+ lftp -f transfer.sh
+ ```
+
+Step-by-step guide for Cadaver
+------------------------------
+
+1. You need to create your UNL
+ <a href="http://Box.com" class="external-link">Box.com</a> account
+ <a href="http://box.unl.edu/" class="external-link">here</a>.
+2. Since we are going to be using
+ <a href="https://en.wikipedia.org/wiki/WebDAV" class="external-link">webdav</a> protocol
+ to access your
+ <a href="http://Box.com" class="external-link">Box.com</a> storage,
+ you need to create an **External Password**. In the
+ <a href="http://Box.com" class="external-link">Box.com</a>
+ interface, you can create it
+ at **<a href="https://unl.app.box.com/settings" class="external-link">Account Settings</a>** > **Create
+ External Password.
+ <span
+ class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/8192521/8126683.png" class="confluence-embedded-image" width="747" height="185" /></span>**
+3. Create a
+ <a href="http://www.mavetju.org/unix/netrc.php" class="external-link">.netrc</a>
+ file in order to automatically login to your box account without
+ typing the password. The file needs to be in your home directory,
+ ie `~/.netrc`. You can easily create this file using the nano text
+ editor by using the command:
+
+ ``` syntaxhighlighter-pre
+ nano ~/.netrc
+ ```
+
+ The file should contain the following lines:
+
+ ``` syntaxhighlighter-pre
+ machine dav.box.com
+ login <box_username>@unl.edu
+ password <external_password>
+ ```
+
+ Once you have typed or pasted these lines into the file, press
+ CTRL-X to exit. Follow the prompts to save the file as `.netrc`.
+
+
+4. Be sure to have the correct permissions on the file. You can change
+ the permissions with the command:
+
+ ``` syntaxhighlighter-pre
+ $ chmod 600 ~/.netrc
+ ```
+
+5. Try out the webdav client by issuing the command:
+
+ ``` syntaxhighlighter-pre
+ $ cadaver https://dav.box.com/dav
+ ```
+
+ It should give you a prompt like:
+
+ ``` syntaxhighlighter-pre
+ dav:/dav/>
+ ```
+
+ Within this prompt, you can view files and navigate through the file
+ system using the usual Bash commands **cd** and **ls**. To download
+ files from Box, use the command:
+
+ ``` syntaxhighlighter-pre
+ get <filename>
+ ```
+
+ Or, alternately, to upload files to your Box, use:
+
+ ``` syntaxhighlighter-pre
+ put <filename>
+ ```
+
+ To exit the prompt, press **ctrl-d**
+
+
+6. Within a submit script, you can upload and download files by using
+ commands such as:
+
+ ``` syntaxhighlighter-pre
+ #!/bin/sh
+ #SBATCH ...
+ ....
+ cat << EOF | cadaver https://dav.box.com/dav
+ get inputfile.txt
+ EOF
+
+ cat << EOF | cadaver https://dav.box.com/dav
+ put outputfile.txt
+ EOF
+ ```
+
+7. The files should automatically appear in your Box account, and be
+ sync'd to your computer if you have the
+ <a href="https://sites.box.com/sync4/" class="external-link">sync client</a>
+ installed.
+
+Related articles
+----------------
+
+- <span class="icon aui-icon aui-icon-small aui-iconfont-page-default"
+ title="Page">Page:</span>
+
+ [Integrating Box with HCC](/display/HCCDOC/Integrating+Box+with+HCC)
+
+- <span class="icon aui-icon aui-icon-small aui-iconfont-page-default"
+ title="Page">Page:</span>
+
+ [Handling Data](/display/HCCDOC/Handling+Data)
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
+Shot 2014-08-14 at 4.55.18 PM.png](attachments/8192521/8126683.png)
+(image/png)
+
+Document generated by Confluence on Oct 24, 2018 14:54
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/handling_data/preventing_file_loss.md b/content/guides/handling_data/preventing_file_loss.md
new file mode 100644
index 00000000..27ddd024
--- /dev/null
+++ b/content/guides/handling_data/preventing_file_loss.md
@@ -0,0 +1,172 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Handling Data](Handling-Data_332256.html)
+
+<span id="title-text"> HCC-DOCS : Preventing File Loss </span>
+==============================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified by
+<span class="editor"> Carrie Brown</span> on Feb 09, 2018
+
+Each research group is allocated 50TB of storage in `/work` on HCC
+clusters. With over 400 active groups, HCC does not have the resources
+to provide regular backups of `/work` without sacrificing the
+performance of the existing filesystem. No matter how careful a user
+might be, there is always the risk of file loss due to user error,
+natural disasters, or equipment failure.
+
+However, there are a number of solutions available for backing up your
+data. By carefully considering the benefits and limitations of each,
+users can select the backup methods that work best for their particular
+needs. For truly robust file backups, we recommend combining multiple
+methods. For example, use Git regularly along with manual backups to an
+external hard-drive at regular intervals such as monthly or biannually.
+
+### 1. Use your local machine:
+
+If you have sufficient hard drive space, regularly backup your `/work`
+directories to your personal computer. To avoid filling up your personal
+hard-drives, consider using an external drive that can easily be placed
+in a fireproof safe or at an off-site location for an extra level of
+protection. To do this, you can either use [Globus
+Connect](https://hcc-docs.unl.edu/display/HCCDOC/Globus+Connect) or an
+SCP client, such
+as <a href="https://cyberduck.io/" class="external-link">Cyberduck</a> or <a href="https://winscp.net/eng/index.php" class="external-link">WinSCP</a>.
+For help setting up an SCP client, check out our [Quick Start
+Guides](https://hcc-docs.unl.edu/display/HCCDOC/Quick+Start+Guides).
+
+For those worried about personal hard drive crashes, UNL
+offers <a href="http://nsave.unl.edu/" class="external-link">the backup service NSave</a>.
+For a small monthly fee, users can install software that will
+automatically backup selected files from their personal machine.
+
+Benefits:
+
+- Gives you full control over what is backed up and when.
+- Doesn't require the use of third party servers (when using SCP
+ clients).
+- Take advantage of our high speed data transfers (10 Gb/s) when using
+ Globus Connect or [setup your SCP client to use our dedicated high
+ speed transfer
+ servers](https://hcc-docs.unl.edu/display/HCCDOC/High-Speed+Data+Transfers)
+
+Limitations:
+
+- The amount you can backup is limited by available hard-drive space.
+- Manual backups of many files can be time consuming.
+
+### 2. Use Git to preserve files and revision history:
+
+Git is a revision control service which can be run locally or can be
+paired with a repository hosting service, such
+as <a href="http://www.github.com/" class="external-link">GitHub</a>, to
+provide a remote backup of your files. Git works best with smaller files
+such as source code and manuscripts. Anyone with an InCommon login can
+utilize <a href="http://git.unl.edu/" class="external-link">UNL's GitLab Instance</a>,
+for free.
+
+Benefits:
+
+- Git is naturally collaboration-friendly, allowing multiple people to
+ easily work on the same project and provides great built-in tools to
+ control contributions and managing conflicting changes.
+- Create individual repositories for each project, allowing you to
+ compartmentalize your work.
+- Using UNL's GitLab instance allows you to create private or internal
+ (accessible by anyone within your organization) repositories.
+
+Limitations:
+
+- Git is not designed to handle large files. GitHub does not allow
+ files larger than 100MB unless using
+ their <a href="https://help.github.com/articles/about-git-large-file-storage/" class="external-link">Git Large File Storage</a> and
+ tracking files over 1GB in size can be time consuming and lead to
+ errors when using other repository hosts.
+
+### 3. Use Attic:
+
+HCC offers
+long-term, <a href="https://en.wikipedia.org/wiki/Nearline_storage" class="external-link">near-line</a> data
+storage
+through [Attic](https://hcc-docs.unl.edu/display/HCCDOC/Using+Attic).
+HCC users with an existing account
+can <a href="http://hcc.unl.edu/attic" class="external-link">apply for an Attic account</a> for
+a <a href="http://hcc.unl.edu/priority-access-pricing" class="external-link">small annual fee</a> that
+is substantially less than other cloud services.
+
+Benefits:
+
+- Attic files are backed up regularly at both HCC locations in Omaha
+ and Lincoln to help provide disaster tolerance and a second security
+ layer against file loss.
+- No limits on individual or total file sizes.
+- High speed data transfers between Attic and the clusters when using
+ Globus Connect and [HCC's high-speed data
+ servers](https://hcc-docs.unl.edu/display/HCCDOC/High-Speed+Data+Transfers).
+
+Limitations:
+
+- Backups must be done manually which can be time consuming. Setting
+ up automated scripts can help speed up this process.
+
+### 4. Use a cloud-based service, such as Box:
+
+Many of us are familiar with services such as Google Drive, Dropbox, Box
+and OneDrive. These cloud-based services provide a convenient portal for
+accessing your files from any computer. NU offers OneDrive and Box
+services to all students, staff and faculty. But did you know that you
+can link your Box account to HCC’s clusters to provide quick and easy
+access to files stored there? [Follow a few set-up
+steps](https://hcc-docs.unl.edu/display/HCCDOC/Integrating+Box+with+HCC) and
+you can add files to and access files stored in your Box account
+directly from HCC clusters. Setup your submit scripts to automatically
+upload results as they are generated or use it interactively to store
+important workflow scripts and maintain a backup of your analysis
+results.
+
+Benefits:
+
+- <a href="http://box.unl.edu/" class="external-link">Box@UNL</a> offers
+ unlimited file storage while you are associated with UNL.
+- Integrating with HCC clusters provides a quick and easy way to
+ automate backups of analysis results and workflow scripts.
+
+Limitations:
+
+- Box has individual file size limitations, larger files will need to
+ be backed up using an alternate method.
+
+### 5. Copy important files to /home:
+
+While `/work` files and directories are not backed up, files and
+directories in `/home` are backed up on a daily basis. Due to the
+limitations of the `/home` filesystem, we strongly recommend that only
+source code and compiled programs are backed up to `/home`. If you do
+use `/home` to backup datasets, please keep a working copy in your
+`/work` directories to prevent negatively impacting the functionality of
+the cluster.
+
+Benefits:
+
+- No need to make manual backups. home files are automatically backed
+ up daily.
+- Files in `/home` are not subject to the 6 month purge policy that
+ exists on `/work`.
+- Doesn't require the use of third-party software or tools.
+
+Limitations:
+
+- Home storage is limited to 20GB per user. Larger files sets will
+ need to be backed up using an alternate method.
+- Home is read-only on the cluster worker nodes so results cannot be
+ directly written or altered from within a submitted job.
+
+
+If you would like more information or assistance in setting up any of
+these methods, contact us
+at <a href="mailto:hcc-support@unl.edu" class="external-link">hcc-support@unl.edu</a>.
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/handling_data/using_attic.md b/content/guides/handling_data/using_attic.md
new file mode 100644
index 00000000..cdb9abe7
--- /dev/null
+++ b/content/guides/handling_data/using_attic.md
@@ -0,0 +1,117 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Handling Data](Handling-Data_332256.html)
+
+<span id="title-text"> HCC-DOCS : Using Attic </span>
+=====================================================
+
+Created by <span class="author"> Zhongtao Zhang</span>, last modified by
+<span class="editor"> Natasha Pavlovikj</span> on Oct 19, 2018
+
+For users who need long-term storage for large amount of data, HCC
+provides an economical solution called Attic. Attic is a reliable
+<a href="https://en.wikipedia.org/wiki/Nearline_storage" class="external-link">near-line data archive</a> storage
+system. The files in Attic can be accessed and shared from anywhere
+using [Globus
+Connect](https://hcc-docs.unl.edu/display/ADMIN/Globus+Connect+Usage),
+with a fast 10Gb/s link. Also, the data in Attic is backed up between
+our Lincoln and Omaha facilities to ensure high availability and
+disaster tolerance. The data and user activities on Attic are subject to
+our
+<a href="http://hcc.unl.edu/hcc-policies" class="external-link">HCC Policies</a>.
+
+Accounts and Cost
+-----------------
+
+To use Attic you will first need an
+<a href="https://hcc.unl.edu/new-user-request" class="external-link">HCC account</a>, and
+then you may apply for an
+<a href="http://hcc.unl.edu/attic" class="external-link">Attic account</a>.
+We charge a small fee per TB per year, but it is cheaper than most
+commercial cloud storage solutions. For the user application form and
+cost, please see the
+<a href="http://hcc.unl.edu/attic" class="external-link">HCC Attic page</a>.
+
+Transfer Files Using Globus Connect
+-----------------------------------
+
+The easiest and fastest way to access Attic is via Globus. You can
+transfer files between your computer, our clusters ($HOME and $WORK on
+Crane, Tusker, and Sandhills), and Attic. Here is a detailed tutorial on
+how to set up and use [Globus Connect](Globus-Connect_6357013.html). For
+Attic, use the Globus Endpoint **hcc\#attic**. Your Attic files are
+located at `~, `which is a shortcut
+for `/attic/<groupname>/<username>`.
+**Note:** *If you are accessing Attic files from your supplementary
+group, you should explicitly set the path to
+/attic/<supplementary\_groupname>/. If you don't do that, by
+default the endpoint will try to place you in your primary group's Attic
+path, which access will be denied if the primary group doesn't have
+Attic allocation.*
+
+Transfer Files Using SCP/SFTP/RSYNC
+-----------------------------------
+
+The transfer server for Attic storage is named `attic.unl.edu`.
+
+**SCP Example**
+
+``` syntaxhighlighter-pre
+$ scp /source/file <username>@attic.unl.edu:~/destination/file
+```
+
+**SFTP example**
+
+``` syntaxhighlighter-pre
+$ sftp <username>@attic.unl.edu
+Password:
+Duo two-factor login for <username>
+Connected to attic.unl.edu.
+sftp> pwd
+Remote working directory: /attic/<groupname>/<username>
+sftp> put source/file destination/file
+sftp> exit
+```
+
+
+
+**RSYNC Example**
+
+``` syntaxhighlighter-pre
+# local to remote rsync command
+$ rsync -avz /local/source/path <username>@attic.unl.edu:remote/destination/path
+
+# remote to local rsync command
+$ rsync -avz <username>@attic.unl.edu:remote/source/path /local/destination/path
+```
+
+
+
+You can also access your data on Attic using our three [high-speed
+transfer servers](High-Speed-Data-Transfers_6946857.html) if you prefer.
+Simply use scp or sftp to connect to one of the transfer servers, and
+your directory is mounted at `/attic/<groupname>/<username>`.
+
+Check Attic Usage
+-----------------
+
+The usage and quota information for your group and the users in the
+group are stored in a filed named "disk\_usage.txt" in your group's
+directory (`/attic/<groupname>`). You can use either Globus Connect or
+scp to download it. Your usage and expiration is also shown in the web
+interface (see below).
+
+Use the web interface
+---------------------
+
+For convenience, a web interface is also provided. Simply go to
+<a href="https://attic.unl.edu" class="external-link">https://attic.unl.edu</a>
+and login with your HCC credentials. Using this interface, you can see
+your quota usage and expiration, manage files, etc. **Please note we do
+not recommend uploading/downloading large files this way**. Use one of
+the other transfer methods above for large datasets.
+
+Document generated by Confluence on Oct 24, 2018 14:54
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/handling_data/using_the_common_file_system.md b/content/guides/handling_data/using_the_common_file_system.md
new file mode 100644
index 00000000..c018c039
--- /dev/null
+++ b/content/guides/handling_data/using_the_common_file_system.md
@@ -0,0 +1,82 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Handling Data](Handling-Data_332256.html)
+
+<span id="title-text"> HCC-DOCS : Using the /common File System </span>
+=======================================================================
+
+Created by <span class="author"> David Swanson</span>, last modified on
+Sep 10, 2018
+
+<span style="color: rgb(0,0,0);">Quick overview: </span>
+--------------------------------------------------------
+
+- Connected read/write to all HCC HPC cluster resources – you will see
+ the same files "in common" on any HCC cluster (i.e. crane, tusker,
+ sandhills)
+- 30 TB Per-group quota at no charge – larger quota available for
+ $100/TB/year
+- No backups are made! Don't be silly! Precious data should still be
+ stored / backed up elsewhere such as on Attic. Please.
+- No purge! So, while your files just might be lost in the case of
+ disk failure or user error, they won't be removed by the purge
+ scripts.
+
+ Accessing common
+
+ <span
+ class="aui-icon aui-icon-small aui-iconfont-info confluence-information-macro-icon"></span>
+ Your /common directory can be accessed via the `$COMMON` environment
+ variable, i.e. `cd $COMMON.`
+
+How should I use /common?
+
+- Store things that are routinely needed on multiple clusters
+- /common is a network attached FS, so limit the number of files per
+ directory (1 million files in a directory is a very bad idea)
+- I**f you are accessing /common for a job, you will need to add a
+ line to your submission script! **
+ - We have each user check out a "license" to access /common for a
+ given job
+ - this allows us to know exactly who is accessing it, and for how
+ long, in case of the need for a shut down so we can try to avoid
+ killing jobs whenever possible
+ - it also allows us to limit how many jobs can hammer this single
+ filesystem so it remains healthy and happy
+
+<span style="color: rgb(0,0,0);">To gain access to the path on worker
+nodes, a job must be </span><span style="color: rgb(0,0,0);">submitted
+with the following SLURM directive:</span>
+
+**SLURM Submit File**
+
+``` syntaxhighlighter-pre
+#SBATCH --licenses=common
+```
+
+<span style="color: rgb(0,0,0);">If a job lacks the above Slurm
+directive, /common will not be accessible from </span><span
+style="color: rgb(0,0,0);">the</span><span
+style="color: rgb(0,0,0);"> worker nodes. (<span
+style="">Briefly</span>, this construct will allow us
+to quickly do maintenance on a single cluster without having to unmount
+$COMMON </span><span style="color: rgb(0,0,0);">from</span><span
+style="color: rgb(0,0,0);"> all HCC resources). </span>
+
+<span style="color: rgb(0,0,0);">What should I **not** do when using /common? </span>
+-------------------------------------------------------------------------------------
+
+- Don't use it for high I/O work flows, use /work for that – /common
+ should mostly be used to read largely static files or data
+- Do not expect your compiled program binaries to work everywhere!
+ /common is available on machines with different cpu architecture,
+ different network connections, and so on. *caveat emptor!*
+ - Serial codes will not be optimized for all clusters
+ - MPI codes, in particular, will likely not work unless recompiled
+ for each cluster
+ - if you use `module `things should be just fine!
+
+Document generated by Confluence on Oct 24, 2018 14:55
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/_index.md b/content/guides/running_applications/_index.md
new file mode 100644
index 00000000..08ae49a4
--- /dev/null
+++ b/content/guides/running_applications/_index.md
@@ -0,0 +1,13 @@
++++
+title = "Running Applications"
+description = "How to run various applications on HCC resources."
+weight = "20"
++++
+
+
+Created by <span class="author"> Adam Caprez</span>, last modified on
+Nov 30, 2016
+
+Document generated by Confluence on Oct 24, 2018 14:48
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/allinea_performance_reports.md b/content/guides/running_applications/allinea_performance_reports.md
new file mode 100644
index 00000000..5a780651
--- /dev/null
+++ b/content/guides/running_applications/allinea_performance_reports.md
@@ -0,0 +1,168 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Running Applications](Running-Applications_7471153.html)
+5. [Allinea Profiling & Debugging Tools](16516466.html)
+
+<span id="title-text"> HCC-DOCS : Allinea Performance Reports </span>
+=====================================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified on
+Jul 10, 2015
+
+| Name | Version | Resource |
+|---------|---------|----------|
+| allinea | 4.2 | tusker |
+| allinea | 5.0 | tusker |
+
+| | | |
+|---------|-----|-------|
+| allinea | 4.2 | crane |
+| allinea | 5.0 | crane |
+
+
+
+<a href="http://www.allinea.com/products/allinea-performance-reports" class="external-link">Allinea Performance Reports</a> is
+a performance evaluation tool that provides a scalable and effective way
+to understand and analyze the performance of applications executed on
+high-performance systems. Allinea Performance Reports can be used with
+any application - no source code, recompilation or instrumentation is
+needed. The main objective of Allinea Performance Reports is to
+determine whether the code fully utilizes the system where it is
+executed and to help developers identify application bottlenecks and
+possible optimizations.
+
+As a result Allinea Performance Reports produces single HTML page report
+with a characterization of the evaluated application. The report
+contains information about the application peak memory usage, and the
+time spent in CPU, MPI/OpenMP and I/O communications. Moreover, the
+report includes information about why the concrete application is
+spending too much time in a particular process and gives tuning advices
+and suggestions of possible application improvements. Allinea
+Performance Reports has low runtime overhead of less than 5%.
+
+Using Allinea Performance Reports on HCC
+========================================
+
+The Holland Computing Center owns **512 Allinea Performance Reports
+licenses** that can be used to evaluate applications executed on Tusker
+and Crane.
+In order to use Allinea Performance Reports on HCC, the appropriate
+module needs to be loaded first. To load the module on Tusker or Crane,
+use
+
+| |
+|-------------------------|
+| module load allinea/5.0 |
+
+Once the module is loaded, Allinea Performance Reports runs by adding
+the **perf-report** command in front of the standard application
+command.
+
+Basic Allinea Performance Reports Usage
+---------------------------------------
+
+The basic usage of **perf-report** is:
+
+**perf-report usage**
+
+``` syntaxhighlighter-pre
+perf-report [OPTION...] PROGRAM [PROGRAM_ARGS]
+or
+perf-report [OPTION...] (mpirun|mpiexec|aprun|...) [MPI_ARGS] PROGRAM [PROGRAM_ARGS]
+```
+
+For example, the command below shows how to run **perf-report** with the
+application “**hello\_world**”:
+
+**perf-report example**
+
+``` syntaxhighlighter-pre
+[<username>@login.tusker ~]$ perf-report ./hello-world
+```
+
+Stdin redirection
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-warning confluence-information-macro-icon"></span>
+
+If your program normally uses the '<' syntax to redirect standard in
+to read from a file, you must use the `--input` option to the
+`perf-report `command instead.
+
+**perf-report stdin redirection**
+
+``` syntaxhighlighter-pre
+[<username>@login.tusker ~]$ perf-report --input=my_input.txt ./hello-world
+```
+
+Allinea Performance Reports Options
+-----------------------------------
+
+More **perf-report** options can be seen by using:
+
+**perf-report options**
+
+``` syntaxhighlighter-pre
+[<username>@login.tusker ~]$ perf-report --help
+```
+
+Some of the most useful options are:
+
+**perf-report useful options**
+
+``` syntaxhighlighter-pre
+--input=FILE (pass the contents of FILE to the target's stdin)
+--nompi, --no-mpi (run without MPI support)
+--mpiargs=ARGUMENTS (command line arguments to pass to mpirun)
+--nodes=NUMNODES (configure the number of nodes for MPI jobs)
+--openmp-threads=NUMTHREADS (configure the number of OpenMP threads for the target)
+-n, --np, --processes=NUMPROCS (specify the number of MPI processes)
+--procs-per-node=PROCS (configure the number of processes per node for MPI jobs)
+```
+
+<span style="line-height: 1.4285715;">
+</span>
+
+<span style="line-height: 1.4285715;">The following pages, </span>[Blast
+with Allinea Performance
+Reports](Blast-with-Allinea-Performance-Reports_11635295.html)<span
+style="line-height: 1.4285715;">, </span>[Ray with Allinea Performance
+Reports](Ray-with-Allinea-Performance-Reports_11635300.html) and [LAMMPS
+with Allinea Performance
+Reports](LAMMPS-with-Allinea-Performance-Reports_11635305.html), <span
+style="line-height: 1.4285715;">show how to run Allinea Performance
+Reports with applications using OpenMP, MPI and standard input/output
+respectively.</span>
+
+
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-warning confluence-information-macro-icon"></span>
+
+**Currently, Allinea Performance Reports works best with compiled
+binaries of an application (for some perl/python files perf-report needs
+to be added in the actual file).**
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[cb\_allinea\_module.xsl](attachments/11635289/11635290.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_allinea\_version.xsl](attachments/11635289/11635291.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/11635289/11635292.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_allinea\_version.xsl](attachments/11635289/11635293.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/11635289/11635294.xml)
+(application/octet-stream)
+
+Document generated by Confluence on Oct 24, 2018 14:48
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/allinea_profiling_debugging_tools.md b/content/guides/running_applications/allinea_profiling_debugging_tools.md
new file mode 100644
index 00000000..00bfb4cb
--- /dev/null
+++ b/content/guides/running_applications/allinea_profiling_debugging_tools.md
@@ -0,0 +1,29 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Running Applications](Running-Applications_7471153.html)
+
+<span id="title-text"> HCC-DOCS : Allinea Profiling & Debugging Tools </span>
+=============================================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified on
+Jun 28, 2016
+
+HCC provides both the Allinea Forge suite and Performance Reports to
+assist with debugging and profiling C/C++/Fortran code. These tools
+support single-threaded, multi-threaded (pthreads/OpenMP), MPI, and CUDA
+code. The Allinea Forge suite consists of two programs: DDT for
+debugging and MAP for profiling. The Performance Reports software
+provides a convenient way to profile HPC applications. It generates an
+easy-to-read single-page HTML report.
+
+For information on using each tool, see the following pages.
+
+[Using Allinea Forge via Reverse
+Connect](Using-Allinea-Forge-via-Reverse-Connect_16516461.html)
+
+[Allinea Performance Reports](Allinea-Performance-Reports_11635289.html)
+
+Document generated by Confluence on Oct 24, 2018 14:48
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/available_software_for_crane.md b/content/guides/running_applications/available_software_for_crane.md
new file mode 100644
index 00000000..1ee3459d
--- /dev/null
+++ b/content/guides/running_applications/available_software_for_crane.md
@@ -0,0 +1,4863 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Running Applications](Running-Applications_7471153.html)
+
+<span id="title-text"> HCC-DOCS : Available Software for Crane </span>
+======================================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified by
+<span class="editor"> Natasha Pavlovikj</span> on Aug 06, 2018
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-approve confluence-information-macro-icon"></span>
+
+HCC provides some software packages via the Singularity container
+software. If you do not see a desired package in the module list below,
+please check the [Using Singularity](Using-Singularity_17040488.html)
+page for the software list there.
+
+Module prerequisites
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-warning confluence-information-macro-icon"></span>
+
+If a module lists one or more prerequisites, the prerequisite module(s)
+must be loaded before or along with, that module.
+
+For example, the `cdo/2.1` modules requires `compiler/pgi/13.` To load
+the cdo module, doing either
+
+`module load compiler/pgi/13module load cdo/2.1`
+
+or
+
+`module load compiler/pgi/13 cdo/2.1` (Note the prerequisite module
+**must** be first.)
+
+is acceptable.
+
+Multiple versions
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-info confluence-information-macro-icon"></span>
+
+Some packages list multiple compilers for prerequisites. This means that
+the package has been built with each version of the compilers listed.
+
+| Name | Version | Module Name | Prerequisites | Type | Domain | Description |
+|------------------------|---------------|----------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-------------|--------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| abacus | 1.0.1 | abacus/1.0 | compiler/intel/13:openmpi/1.8 | library | runtime support | |
+| abaqus | 6.14.2 | abaqus/6.14.2 | None | application | Engineering | Abaqus is a software suite for finite element analysis and computer-aided engineering. |
+| abinit | 8.0.8 | abinit/8.0 | compiler/intel/12:openmpi/1.8 | application | computational chemistry | ABINIT is a package whose main program allows one to find the total energy. |
+| abinit | 8.4.2 | abinit/8.4 | compiler/intel/15:openmpi/1.10 | application | computational chemistry | ABINIT is a package whose main program allows one to find the total energy. |
+| abyss | 2.1.0 | abyss/2.1 | compiler/gcc/6.1:openmpi/2.1 | application | bioinformatics | ABySS is a de novo sequence assembler intended for short paired-end reads and large genomes. |
+| aligngraph | 1.0 | aligngraph/1.0 | None | application | computational biology | |
+| allpathslg | Latest | allpathslg/latest | compiler/gcc/4.7 | application | biology | |
+| anaconda | 2.7 | anaconda/2.7 | None | application | system | |
+| anaconda | 3.3 | anaconda/3.3 | None | application | system | |
+| anaconda | 3.4 | anaconda/3.4 | None | application | system | |
+| anaconda | 4.3 | anaconda/4.3 | None | application | system | |
+| art | 2.6.0 | art/2.6 | None | application | computational biology | ART is a set of simulation tools to generate synthetic next-generation sequencing reads. |
+| asreml | 3.0 | asreml/3.0 | None | application | data analysis | ASReml |
+| asreml | 4.1 | asreml/4.1 | None | application | data analysis | ASReml |
+| atk | 13.8.2 | atk/13.8.2 | compiler/gcc/4.7:mpich2/1.5 | application | Chemistry | |
+| atk | 2014.1 | atk/2014.1 | compiler/gcc/4.7:mpich2/1.5 | application | Chemistry | |
+| atk | 2015.1 | atk/2015.1 | compiler/gcc/4.7:mpich2/1.5 | application | Chemistry | |
+| atk | 2016.3 | atk/2016.3 | compiler/gcc/4.7:mpich2/1.5 | application | Chemistry | |
+| augustus | 3.0 | augustus/3.0 | compiler/gcc/4.9 None | application | computational biology | AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. |
+| automake | 1.14 | automake/1.14 | None | application | Utilities | Automake is a tool for automatically generating Makefile.in files compliant with the GNU Coding Standards. |
+| automake | 1.15 | automake/1.15 | None | application | Utilities | Automake is a tool for automatically generating Makefile.in files compliant with the GNU Coding Standards. |
+| ballgown | 2.2.0 | ballgown/2.2 | None | application | computational biology | Ballgown is a software package designed to facilitate flexible differential expression analysis of RNA-Seq data. It also provides functions to organize, visualize, and analyze the expression measurements for your transcriptome assembly. |
+| bam-readcount | 0.6 | bam-readcount/0.6 | None | application | computational biology | The purpose of this program is to generate metrics at single nucleotide positions. |
+| bayespeak | 1.24.0 | bayespeak/1.24.0 | None | application | computational biology | This package is an implementation of the BayesPeak algorithm for peak-calling in ChIP-seq data. |
+| bcftools | 1.1 | bcftools/1.1 | compiler/gcc/4.8 | application | computational biology | BCF Tools - a generic tool for the Variant Call Format(VCF) |
+| bcftools | 1.2 | bcftools/1.2 | compiler/gcc/4.8 | application | computational biology | BCF Tools - a generic tool for the Variant Call Format(VCF) |
+| bcl2fastq | 1.8.4 | bcl2fastq/1.8 | None | application | biology | bcl2fastq can be used to demultiplex data and convert BCL files to FASTQ file formats for downstream analysis |
+| bcl2fastq | 2.17 | bcl2fastq/2.17 | compiler/gcc/4.7 | application | biology | bcl2fastq can be used to demultiplex data and convert BCL files to FASTQ file formats for downstream analysis |
+| BICseq | 1.1.2 | BICseq/1.1 | None | application | computational biology | BIC-seq can accurately and efficiently identify CNVs via minimizing the Bayesian information criterion. |
+| bioperl | 1.6 | bioperl/1.6 | None | application | computational biology | BioPerl is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications |
+| biopieces | 1.0 | biopieces/1.0 | compiler/gcc/4.8:openmpi/1.6 | application | computational biology | The Biopieces are a collection of bioinformatics tools that can be pieced together in a very easy and flexible manner to perform both simple and complex tasks. |
+| biosamtools | 1.38 | biosamtools/1.38 | None | application | computational biology | |
+| bismark | 0.14.2 | bismark/0.14 | None | application | computational biology | Bisulfite read mapper and methylation caller. |
+| bismark | 0.19.0 | bismark/0.19 | None | application | computational biology | Bisulfite read mapper and methylation caller. |
+| blast | 2.2.29 | blast/2.2.29 | None | application | computational biology | NCBI BLAST+ sequence alignment package. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. |
+| blast | 2.2.30 | blast/2.2 | None | application | computational biology | NCBI BLAST+ sequence alignment package. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. |
+| blast | 2.4.0 | blast/2.4 | None | application | computational biology | NCBI BLAST+ sequence alignment package. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. |
+| blast-legacy | 2.2.26 | blast-legacy/2.2.26 | None | application | computational biology | NCBI BLAST sequence alignment package. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. |
+| blat | 34 | blat/34 | None | application | computational biology | Blat is an alignment tool like BLAST, but it is structured differently. On DNA, Blat works by keeping an index of an entire genome in memory. Thus, the target database of BLAT is not a set of GenBank sequences, but instead an index derived from the assembly of the entire genome. |
+| blat | 35x1 | blat/35x1 | None | application | computational biology | Blat is an alignment tool like BLAST, but it is structured differently. On DNA, Blat works by keeping an index of an entire genome in memory. Thus, the target database of BLAT is not a set of GenBank sequences, but instead an index derived from the assembly of the entire genome. |
+| boost | 1.44 | boost/1.44 | compiler/gcc/4.9 None | application | System Environment/Base | Boost provides free peer-reviewed portable C++ source libraries. |
+| boost | 1.54 | boost/1.54 | compiler/gcc/4.9 | application | System Environment/Base | Boost provides free peer-reviewed portable C++ source libraries. |
+| boost | 1.55 | boost/1.55 | compiler/gcc/4.9:openmpi/1.10 | application | System Environment/Base | Boost provides free peer-reviewed portable C++ source libraries. |
+| boost | 1.55.0 | boost/1.55.0 | None | application | System Environment/Base | Boost provides free peer-reviewed portable C++ source libraries. |
+| boost | 1.57 | boost/1.57 | compiler/gcc/4.9 | application | System Environment/Base | Boost provides free peer-reviewed portable C++ source libraries. |
+| boost | 1.59 | boost/1.59 | compiler/gcc/4.9 compiler/gcc/5.4 compiler/gcc/6.1 compiler/intel/13 | application | System Environment/Base | Boost provides free peer-reviewed portable C++ source libraries. |
+| boost | 1.63 | boost/1.63 | compiler/gcc/6.1 compiler/intel/16 | application | System Environment/Base | Boost provides free peer-reviewed portable C++ source libraries. |
+| boost | 1.64 | boost/1.64 | compiler/gcc/7.1 | application | System Environment/Base | Boost provides free peer-reviewed portable C++ source libraries. |
+| boost | 1.66 | boost/1.66 | compiler/gcc/7.1 compiler/gcc/8.2 | application | System Environment/Base | Boost provides free peer-reviewed portable C++ source libraries. |
+| bowtie | 1.0 | bowtie/1.0 | None | application | computational biology | Ultrafast, memory-efficient short read aligner |
+| bowtie | 1.1.2 | bowtie/1.1 | None | application | computational biology | Ultrafast, memory-efficient short read aligner |
+| bowtie | 2.2.6 | bowtie/2.2 | None | application | computational biology | Ultrafast, memory-efficient short read aligner |
+| bowtie | 2.3.4 | bowtie/2.3 | None | application | computational biology | Bowtie2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. |
+| bwa | 0.6.2 | bwa/0.6 | None | application | computational biology | bwa - Burrows-Wheeler Alignment Tool |
+| bwa | 0.7 | bwa/0.7 | None | application | computational biology | bwa - Burrows-Wheeler Alignment Tool |
+| bzip2 | 1.0 | bzip2/1.0 | None | library | runtime support | |
+| caffe | 1.0 | caffe/1.0 | None | application | package | It is developed by the Berkeley Vision and Learning Center (BVLC) and by community contributors. Yangqing Jia created the project during his PhD at UC Berkeley. Caffe is released under the BSD 2-Clause license. |
+| cap3 | 122107 | cap3/122107 | None | application | computational biology | CAP3: A DNA Sequence Assembly Program |
+| carlsim | 3.1 | carlsim/3.1 | None | application | computational biology | CARLsim is an efficient, easy-to-use, GPU-accelerated software framework for simulating large-scale spiking neural network (SNN) models with a high degree of biological detail. |
+| carlsim | 4.0 | carlsim/4.0 | None | application | computational biology | CARLsim is an efficient, easy-to-use, GPU-accelerated software framework for simulating large-scale spiking neural network (SNN) models with a high degree of biological detail. |
+| ccp4 | 7.0 | ccp4/7.0 | None | application | unknown | |
+| cd-hit | 4.6 | cd-hit/4.6 | None | application | computational biology | cd-hit is a very widely used program for clustering and comparing protein or nucleotide sequences. |
+| cdna-cupcake-tofu2 | 5.2 | cdna-cupcake-tofu2/5.2 | None | application | computational biology | cDNA\_Cupcake is a miscellaneous collection of Python and R scripts used for analyzing sequencing data. |
+| cdo | 1.6 | cdo/1.6 | compiler/pgi/13 | library | runtime support | |
+| cdo | 1.7.1 | cdo/1.7 | compiler/intel/15 compiler/pgi/14 compiler/pgi/15 | library | runtime support | |
+| cdo | 1.8 | cdo/1.8 | compiler/pgi/13 | library | runtime support | |
+| cdo | 1.8.1 | cdo/1.8 | compiler/intel/15 compiler/intel/16 compiler/pgi/14 compiler/pgi/15 | library | runtime support | |
+| cexor | 1.10 | cexor/1.10 | None | application | computational biology | An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates. |
+| clark | 1.2 | clark/1.2 | None | application | computational biology | |
+| clearcut | 1.0 | clearcut/1.0 | None | application | computational biology | Clearcut - The reference implementation for Relaxed Neighbor Joining (RNJ) |
+| clustal-omega | 1.2 | clustal-omega/1.2 | None | application | computational biology | Clustal Omega is the latest addition to the Clustal family. It offers a significant increase in scalability over previous versions, allowing hundreds of thousands of sequences to be aligned in only a few hours |
+| CNVnator | 0.3 | CNVnator/0.3 | compiler/gcc/4.9 | application | genotyping | CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. |
+| cogent | 3.1 | cogent/3.1 | None | application | computational biology | Cogent is a tool for reconstructing the coding genome using high-quality full-length transcriptome sequences. |
+| compiler/gcc | 4.7 | compiler/gcc/4.7 | None | application | compiler | |
+| compiler/gcc | 4.8 | compiler/gcc/4.8 | None | application | compiler | |
+| compiler/gcc | 4.9 | compiler/gcc/4.9 | None | application | compiler | |
+| compiler/gcc | 5.4 | compiler/gcc/5.4 | None | application | compiler | |
+| compiler/gcc | 6.1 | compiler/gcc/6.1 | None | application | compiler | |
+| compiler/gcc | 7.1 | compiler/gcc/7.1 | None | application | compiler | |
+| compiler/gcc | 8.2 | compiler/gcc/8.2 | None | application | compiler | |
+| compiler/intel | 12 | compiler/intel/12 | None | application | compiler | |
+| compiler/intel | 13 | compiler/intel/13 | None | application | compiler | |
+| compiler/intel | 15 | compiler/intel/15 | None | application | compiler | |
+| compiler/intel | 16 | compiler/intel/16 | None | application | compiler | |
+| compiler/intel | 18 | compiler/intel/18 | None | application | compiler | |
+| compiler/pgi | 12 | compiler/pgi/12 | None | application | compiler | |
+| compiler/pgi | 13 | compiler/pgi/13 | None | application | compiler | |
+| compiler/pgi | 14 | compiler/pgi/14 | None | application | compiler | |
+| compiler/pgi | 15 | compiler/pgi/15 | None | application | compiler | |
+| compiler/pgi | 16 | compiler/pgi/16 | None | application | compiler | |
+| cp2k | 2.6 | cp2k/2.6 | compiler/gcc/4.7:openmpi/1.8 | library | runtime support | |
+| cp2k | 3.0 | cp2k/3.0 | compiler/gcc/4.7:openmpi/1.8 | library | runtime support | |
+| cp2k | 4.1 | cp2k/4.1 | compiler/gcc/4.7:openmpi/1.8 | library | runtime support | |
+| cp2k | 5.1 | cp2k/5.1 | compiler/gcc/4.7:openmpi/1.8 | library | runtime support | |
+| crest | 1.0 | crest/1.0 | None | application | computational biology | |
+| csaw | 1.4 | csaw/1.4 | None | application | computational biology | Detection of differentially bound regions in ChIP-seq data with sliding windows, with methods for normalization and proper FDR control. |
+| cuda | 6.0 | cuda/6.0 | None | application | compiler | NVIDIA CUDA Toolkit for Linux. |
+| cuda | 6.5 | cuda/6.5 | None | application | compiler | NVIDIA CUDA Toolkit for Linux. |
+| cuda | 7.5 | cuda/7.5 | None | application | compiler | NVIDIA CUDA Toolkit for Linux. |
+| cuda | 8.0 | cuda/8.0 | None | application | compiler | NVIDIA CUDA Toolkit for Linux. |
+| cuda | 9.0 | cuda/9.0 | None | application | compiler | NVIDIA CUDA Toolkit for Linux. |
+| cuda | 9.1 | cuda/9.1 | None | application | compiler | NVIDIA CUDA Toolkit for Linux. |
+| cudnn | v5 | cudnn/v5 | None | application | compiler | NVIDIA cuDNN Toolkit for Linux. |
+| cufflinks | 2.1 | cufflinks/2.1 | None | application | computational biology | cufflinks - Transcript assembly, differential expression, and differential regulation for RNA-Seq |
+| cufflinks | 2.2 | cufflinks/2.2 | None | application | computational biology | cufflinks - Transcript assembly, differential expression, and differential regulation for RNA-Seq |
+| curl | 7.50 | curl/7.50 | None | application | network | |
+| cytoscape | 3.6 | cytoscape/3.6 | None | application | unknown | Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data. |
+| diffsplice | 0.1.11 | diffsplice/0.1 | None | application | computational biology | DiffSplice: the Genome-Wide Detection of Differential Splicing Events with RNA-seq |
+| dmtcp | 2.0 | dmtcp/2.0 | None | application | Utility | |
+| dmtcp | 2.3 | dmtcp/2.3 | None | application | Utility | |
+| dmtcp | 2.4 | dmtcp/2.4 | None | application | Utility | |
+| dmtcp | 2.5 | dmtcp/2.5 | None | application | Utility | |
+| ea-utils | 1.01 | ea-utils/1.0 | None | application | computational biology | EA Utils is a collection of command line tools for processing NextGen sequencing data. Included are fastq-stats and sam-stats which are lightweight tools that display a variety of statistics on fastq and sam files. |
+| elk | 4.3.6 | elk/4.3 | compiler/intel/13:openmpi/1.8 | library | runtime support | |
+| emacs | 24.5 | emacs/24.5 | None | application | unknown | |
+| emboss | 6.5.7 | emboss/6.5 | None | application | computational biology | EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. |
+| erne | 2.1.1 | erne/2.1 | None | application | computational biology | ERNE is a short string alignment package whose goal is to provide an all-inclusive set of tools to handle short (NGS-like) reads. |
+| esmf | 5.2.0rp3 | esmf/5.2 | compiler/intel/13 | library | runtime support | |
+| espresso | 5.0 | espresso/5.0 | compiler/intel/13:openmpi/1.8 | library | runtime support | |
+| espresso | 6.2.1 | espresso/6.2 | compiler/intel/15:openmpi/2.0 | library | runtime support | |
+| exomiser | 7.2 | exomiser/7.2 | None | application | computational biology | The Exomiser is a Java program that finds potential disease-causing variants from whole-exome or whole-genome sequencing data. |
+| exonerate | 2.2 | exonerate/2.2 | None | application | computational biology | Exonerate - a generic tool for sequence alignment. |
+| express | 1.5 | express/1.5 | None | application | life sciences | express - Streaming quantification for high-throughput sequencing |
+| fastqc | 0.10 | fastqc/0.10 | None | application | computational biology | fastqc - A Quality Control application for FastQ files |
+| fastx\_toolkit | 0.0.14 | fastx\_toolkit/0.0.14 | None | application | computational biology | FASTX Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. |
+| fftw2 | 2.1 | fftw2/2.1 | compiler/gcc/4.8 compiler/intel/13 | library | runtime support | |
+| fftw3 | 3.3 | fftw3/3.3 | compiler/gcc/4.8 compiler/gcc/4.8:openmpi/1.8 compiler/gcc/4.9 compiler/gcc/6.1:openmpi/2.0 compiler/intel/12 compiler/intel/12:openmpi/1.8 compiler/intel/13 compiler/intel/13:openmpi/1.8 compiler/intel/15 | library | runtime support | |
+| flash | 1.2.11 | flash/1.2 | compiler/gcc/4.9 | application | computational biology | FLASH (Fast Length Adjustment of SHort reads) is a very fast and accurate software tool to merge paired-end reads from next-generation sequencing experiments. FLASH is designed to merge pairs of reads when the original DNA fragments are shorter than twice the length of reads. The resulting longer reads can significantly improve genome assemblies. They can also improve transcriptome assembly when FLASH is used to merge RNA-seq data. |
+| gamess | 20141205R1 | gamess/20141205R1 | compiler/intel/13:openmpi/1.8 | library | runtime support | |
+| gatk | 3.4-46 | gatk/3.4 | None | application | computational biology | The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyze high-throughput sequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size. |
+| gatk | 3.7 | gatk/3.7 | None | application | computational biology | The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyze high-throughput sequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size. |
+| gcprofile | 1.0 | gcprofile/1.0 | None | application | computational biology | GC-Profile is a web-based tool for visualizing and analyzing the variation of GC content in genomic sequences |
+| gctb | 1.0 | gctb/1.0 | compiler/gcc/4.9:openmpi/1.10 | library | runtime support | |
+| gdal | 1.11 | gdal/1.11 | compiler/gcc/4.9 | library | runtime support | |
+| gdcclient | 1.2.0 | gdcclient/1.2 | compiler/gcc/4.9 | library | runtime support | |
+| genemark-es | 2.3f | genemark-es/2.3f | None | application | computational biology | GeneMark-ES. |
+| genemarks | 2.5p | genemarks/2.5p | None | application | computational biology | GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions |
+| genemarks | 4.3 | genemarks/4.3 | None | application | computational biology | GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions |
+| geos | 3.5 | geos/3.5 | compiler/gcc/4.9 | library | runtime support | |
+| gflags | 2.1 | gflags/2.1 | None | library | unknown | Online documentation available at: https://gflags.github.io/gflags/ |
+| glog | 0.3.3 | glog/0.3 | None | application | Utility | |
+| grib-api | 1.12.3 | grib-api/1.12 | compiler/intel/13 | library | runtime support | |
+| grib-api | 1.14.5 | grib-api/1.14 | compiler/intel/15 compiler/pgi/14 compiler/pgi/15 | library | runtime support | |
+| gromacs | 4.6 | gromacs/4.6 | compiler/gcc/4.8:openmpi/1.6 | library | runtime support | |
+| gromacs | 5.1.4 | gromacs/5.1 | compiler/gcc/4.9:openmpi/2.0 | application | computational biology | GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. |
+| GSL | 1.16 | GSL/1.16 | compiler/gcc/4.9 compiler/intel/13 | library | runtime support | |
+| gtool | 0.7.5 | gtool/0.7 | compiler/gcc/6.1 | application | computational biology | GTOOL is a program for transforming sets of genotype data for use with the programs SNPTEST and IMPUTE. |
+| hapflk | 1.3.0 | hapflk/1.3 | None | application | package | hapflk is a software implementing the hapFLK \[1\] and FLK \[2\] tests for the detection of selection signatures based on multiple population genotyping data. |
+| harminv | 1.4 | harminv/1.4 | compiler/gcc/4.9 | library | runtime support | |
+| haskell-platform | 8.2.1 | haskell-platform/8.2.1 | None | application | Utilities | The Haskell Platform is a collection of software packages, tools and libraries that create a common platform for using and developing applications in Haskell.. |
+| hdf4 | 4.2 | hdf4/4.2 | compiler/gcc/4.7 compiler/gcc/4.8 compiler/gcc/4.9 compiler/intel/12 compiler/intel/13 compiler/intel/15 compiler/intel/16 compiler/pgi/12 compiler/pgi/13 compiler/pgi/14 compiler/pgi/15 | library | runtime support | |
+| hdf5 | 1.8 | hdf5/1.8 | compiler/gcc/4.7 compiler/gcc/4.8 compiler/gcc/4.9 compiler/intel/12 compiler/intel/13 compiler/pgi/12 compiler/pgi/13 compiler/pgi/14 compiler/pgi/15 None | library | runtime support | |
+| hdf5 | 1.8.15 | hdf5/1.8 | compiler/intel/15 compiler/intel/16 | library | runtime support | |
+| hiddendomains | 2.3 | hiddendomains/2.3 | None | application | chip-seq | hiddenDomains is a suite of programs used to identify significant enrichment of ChIP-seq reads that span large domains. |
+| hisat2 | 2.0.5 | hisat2/2.0 | None | application | computational biology | HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). |
+| hmmer | 3.1 | hmmer/3.1 | compiler/gcc/4.8:openmpi/1.6 compiler/gcc/4.8:openmpi/1.8 | application | computational biology | HMMER biosequence analysis using profile hidden Markov models |
+| htslib | 1.3.2 | htslib/1.3 | None | application | computational biology | HTSlib is an implementation of a unified C library for accessing common file formats. |
+| HTSlib | 1.2 | HTSlib/1.2 | compiler/gcc/4.8 | application | computational biology | HTSlib - the core library used by samtools and bcftools. |
+| humann2 | 0.9.9 | humann2/0.9 | None | application | computational biology | HUMAnN2 is the next generation of HUMAnN (HMP Unified Metabolic Analysis Network). |
+| idba | 1.1.3 | idba/1.1 | None | application | computational biology | IDBA is a practical iterative De Bruijn Graph De Novo Assembler for sequence assembly in bioinfomatics. |
+| idr | 2.0 | idr/2.0 | None | application | computational biology | The IDR (Irreproducible Discovery Rate) framework is a uni�ed approach to measure the reproducibility of �ndings identi�ed from replicate experiments and provide highly stable thresholds based on reproducibility. |
+| igraph | 0.7 | igraph/0.7 | compiler/gcc/4.9 | library | runtime support | |
+| ima2p | 1.0 | ima2p/1.0 | compiler/gcc/6.1:openmpi/1.10 | application | Bayesian MCMC | IMa2p is a parallel implementation of IMa2, using OpenMPI-C++ - a Bayesian MCMC based method for inferring population demography under the IM (Isolation with Migration) model. |
+| intel-mkl | 12 | intel-mkl/12 | None | library | tools | Numerical library, contains blas/lapack |
+| intel-mkl | 13 | intel-mkl/13 | None | library | tools | Numerical library, contains blas/lapack |
+| intel-mkl | 15 | intel-mkl/15 | None | library | tools | Numerical library, contains blas/lapack |
+| intel-mkl | 16 | intel-mkl/16 | None | library | tools | Numerical library, contains blas/lapack |
+| interproscan | 5.23-62.0 | interproscan/5.23 | compiler/gcc/4.8 | application | computational biology | Scans a range of protein signatures against your sequences and provides protein functional analysis. |
+| interproscan | 5.24-63.0 | interproscan/5.24 | compiler/gcc/4.8 | application | computational biology | Scans a range of protein signatures against your sequences and provides protein functional analysis. |
+| interproscan | 5.8-49.0 | interproscan/5.8 | None | application | computational biology | Scans a range of protein signatures against your sequences and provides protein functional analysis. |
+| irods | 4.1 | irods/4.1 | None | application | unknown | The integrated Rule-Oriented Data System (iRODS) is open source data management software used by research organizations and government agencies worldwide. This module includes the icommands client programs only. |
+| jags | 3.4 | jags/3.4 | compiler/intel/15 | application | mathematics | JAGS is Just Another Gibbs Sampler. |
+| jags | 4.2 | jags/4.2 | compiler/gcc/4.9 compiler/intel/15 | application | mathematics | JAGS is Just Another Gibbs Sampler. |
+| jags | 4.3 | jags/4.3 | compiler/intel/15 | application | mathematics | JAGS is Just Another Gibbs Sampler. |
+| jellyfish | 2.2.0 | jellyfish/2.2 | None | application | computational biology | Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. |
+| jellyfish | 2.2.7 | jellyfish/2.2 | compiler/gcc/4.9 | application | computational biology | Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. |
+| jmosaics | 1.10 | jmosaics/1.10 | None | application | computational biology | Joint analysis of multiple ChIP-Seq data sets. |
+| julia | 0.6.2 | julia/0.6 | None | application | Language | Julia is a high-level, high-performance dynamic programming language for numerical computing. |
+| kaiju | 1.4.4 | kaiju/1.4 | compiler/gcc/4.9 | library | runtime support | |
+| kaiju | 1.5.0 | kaiju/1.5 | compiler/gcc/4.9 | application | Bioinformatics | |
+| kalign | 2.03 | kalign/2.03 | None | application | computational biology | Kalign is a fast and accurate multiple sequence alignment algorithm designed to align large numbers of protein sequences. |
+| kallisto | 0.42.3 | kallisto/0.42 | compiler/gcc/4.8 | library | runtime support | |
+| khmer | 2.0 | khmer/2.0 | None | application | computational biology | Khmer is tools for in-memory nucleotide sequence k-mer counting, filtering, graph traversal and more. |
+| kraken | 1.0 | kraken/1.0 | None | application | computational biology | Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. |
+| lammps | 10Aug2015 | lammps/10Aug2015 | compiler/intel/15:openmpi/1.8 | library | runtime support | |
+| lammps | 10Feb2017 | lammps/10Feb2017 | compiler/gcc/6.1:openmpi/2.0 compiler/intel/15:openmpi/1.10 | library | runtime support | |
+| lammps | 15MAY2015 | lammps/15May15 | compiler/gcc/4.9:openmpi/1.8 compiler/gcc/4.9:openmpi/2.1 | library | runtime support | |
+| lammps | 30Oct2014 | lammps/30Oct2014 | compiler/gcc/4.8:openmpi/1.8 | library | runtime support | |
+| lammps | 31Jan2014 | lammps/31Jan2014 | compiler/gcc/4.8:openmpi/1.6 | library | runtime support | |
+| largenet | 0.6 | largenet/0.6 | compiler/gcc/4.9 | library | runtime support | |
+| last | 1.0 | last/1.0 | compiler/gcc/4.9 | library | runtime support | |
+| libctl | 3.2 | libctl/3.2 | compiler/gcc/4.9 compiler/gcc/6.1 | library | runtime support | |
+| libint | 1.1 | libint/1.1 | compiler/gcc/4.7 | application | Computational Chemistry | Libint is a software stack for computing integrals used in molecular quantum mechanics |
+| libxc | 2.2.3 | libxc/2.2 | compiler/intel/13 | library | runtime support | |
+| libxml2 | 2.7 | libxml2/2.7 | compiler/gcc/4.9 | library | runtime support | |
+| libxml2 | 2.9 | libxml2/2.9 | compiler/gcc/4.9 | library | runtime support | |
+| libxslt | 1.1 | libxslt/1.1 | compiler/gcc/4.9 | library | runtime support | |
+| LIS | 7.0r | LIS/7.0r | compiler/intel/13:openmpi/1.8 | library | runtime support | |
+| lmdb | 0.9 | lmdb/0.9 | None | library | unknown | Lightning memory-mapped database library. |
+| lmod | lmod | lmod/lmod | None | application | unknown | Lmod: An Environment Module System |
+| lofreq | 2.1.3.1 | lofreq/2.1 | None | application | computational biology | LoFreq is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. |
+| lsdyna | 10.0 | lsdyna/10.0 | None | application | unknown | |
+| lsdyna | 10.1 | lsdyna/10.1 | None | application | unknown | |
+| lsdyna | 5.1.1 | lsdyna/5.1.1 | None | application | unknown | |
+| lsdyna | 6.0.0 | lsdyna/6.0.0 | None | application | unknown | |
+| lsdyna | 6.1.2 | lsdyna/6.1.2 | None | application | unknown | |
+| lsdyna | 7.0.0 | lsdyna/7.0.0 | None | application | unknown | |
+| lsdyna | 7.1.1 | lsdyna/7.1.1 | None | application | unknown | |
+| lsdyna | 8.0.0 | lsdyna/8.0.0 | None | application | unknown | |
+| lsdyna | 8.0.1 | lsdyna/8.0.1 | None | application | unknown | |
+| lsdyna | 8.1.0 | lsdyna/8.1.0 | None | application | unknown | |
+| lsdyna | 9.0.1 | lsdyna/9.0.1 | None | application | unknown | |
+| lsdyna | 9.2.0 | lsdyna/9.2.0 | None | application | unknown | |
+| m4 | 1.4 | m4/1.4 | None | application | Utilities | GNU M4 is an implementation of the traditional Unix macro processor. |
+| mafft | 7.149 | mafft/7.149 | None | application | biology | Multiple alignment program for amino acid or nucleotide sequences |
+| maq | 0.7 | maq/0.7 | None | application | computational biology | maq - Mapping and Assembly with Quality. |
+| matio | 1.5 | matio/1.5 | compiler/gcc/4.9 | library | runtime support | |
+| mauve | 2.4 | mauve/2.4 | None | application | computational biology | mauve - Multiple Genome Alignment. |
+| maven | 3.2 | maven/3.2 | None | application | system | Apache Maven is a software project management and comprehension tool. |
+| maven | 3.5 | maven/3.5 | None | application | system | Apache Maven is a software project management and comprehension tool. |
+| meep | 1.3 | meep/1.3 | None | library | runtime support | |
+| meep\_parallel | 1.3 | meep\_parallel/1.3 | compiler/gcc/4.9:openmpi/1.10 | library | runtime support | |
+| meerkat | 0.189 | meerkat/0.1 | None | application | computational biology | Meerkat is designed to identify structural variations |
+| megahit-gpu | 1.1 | megahit-gpu/1.1 | None | application | computational biology | MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. |
+| MEME | 4.11.3 | MEME/4.11 | None | application | computational biology | The MEME suite is a collection of tools for the discovery and analysis of sequence motifs. It is hosted at http://meme-suite.org/. |
+| meme-suite | 4.12.0 | meme-suite/4.12 | compiler/gcc/6.1:openmpi/2.0 | application | computational biology | |
+| MET | 5.0 | MET/5.0 | None | library | runtime support | |
+| metaphlan | 1.7 | metaphlan/1.7 | None | application | computational biology | MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. |
+| metaphlan | 2.6.0 | metaphlan/2.6 | None | application | metagenomic phylogenetic analysis | MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. |
+| metavelvet | 1.2.01 | metavelvet/1.2 | None | application | computational biology | MetaVelvet is an extension of Velvet assembler to de novo metagenome assembly from short sequence reads. |
+| miRDeep | 2.0.0 | miRDeep/2.0 | None | application | computational biology | miRDeep2 is a completely overhauled tool which discovers microRNA genes by analyzing sequenced RNAs. |
+| misis | 1.0 | misis/1.0 | None | application | computational biology | |
+| modeller | 9.19 | modeller/9.19 | None | application | unknown | |
+| mongodb-client | 3.2 | mongodb-client/3.2 | None | application | Utility | Client programs for MongoDB. |
+| mongodb-client | 3.4 | mongodb-client/3.4 | None | application | Utility | Client programs for MongoDB. |
+| mono | 4.6 | mono/4.6 | None | application | compiler | Mono is an open source implementation of Microsoft's .NET Framework based on the ECMA standards for C\# and the Common Language Runtime. |
+| mono | 5.10 | mono/5.10 | None | application | compiler | Mono is an open source implementation of Microsoft's .NET Framework based on the ECMA standards for C\# and the Common Language Runtime. |
+| moose | 1.0 | moose/1.0 | compiler/gcc/6.1:openmpi/2.0 | library | runtime support | |
+| mosaik | 2.2 | mosaik/2.2 | None | application | computational biology | MOSAIK is a reference-guided aligner for next-generation sequencing technologies. |
+| mothur | 1.35.1 | mothur/1.35 | compiler/gcc/4.9:openmpi/1.10 | library | runtime support | |
+| mpb | 1.5 | mpb/1.5 | compiler/gcc/6.1:openmpi/2.0 | library | runtime support | |
+| mpiblast | 1.6 | mpiblast/1.6 | compiler/gcc/4.8:openmpi/1.6 | application | computational biology | mpiBLAST is a freely available, open-source, parallel implementation of NCBI BLAST. |
+| mpich2 | 1.5 | mpich2/1.5 | compiler/gcc/4.7 | library | runtime support | |
+| mplus | 6.12 | mplus/6.12 | None | application | unknown | Mplus is a latent variable modeling program with a wide variety of analysis capabilities. |
+| mplus | 7.0 | mplus/7.0 | None | application | unknown | Mplus is a latent variable modeling program with a wide variety of analysis capabilities. |
+| mugsy | v1r2.3 | mugsy/v1r2.3 | None | application | computational biology | |
+| multiqc | 0.8 | multiqc/0.8 | None | application | computational biology | Aggregate results from bioinformatics analyses across many samples into a single report |
+| multiwell | 2017 | multiwell/2017 | compiler/gcc/6.1:openmpi/2.1 | application | chemistry | MultiWell calculates time dependent concentrations, reaction yields, vibrational distributions, and rate constants as functions of temperature and pressure for multi-well, multi-channel unimolecular reactions systems that consist of stable species and multiple isomerization and/or dissociation reactions. |
+| mummer | 3.23 | mummer/3.23 | None | application | computational biology | MUMmer - A modular system for the rapid whole genome alignment of finished or draft sequence |
+| muscle | 3.8 | muscle/3.8 | None | application | computational biology | Popular multiple alignment software |
+| music | 1.0 | music/1.0 | None | application | computational biology | MUSIC is an algorithm for identification of enriched regions at multiple scales in the read depth signals from ChIP-Seq experiments. |
+| mutect | 1.1 | mutect/1.1 | None | application | computational biology | MuTect is a method developed at the Broad Institute for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes. |
+| mvapich2 | 1.9 | mvapich2/1.9 | compiler/intel/13 | library | runtime support | |
+| mytaxa | 1.0 | mytaxa/1.0 | None | application | computational biology | MyTaxa - Assign taxonomy to metagenomic fragments. |
+| namd | 2.12 | namd/2.12 | compiler/gcc/4.9:openmpi/1.10 | library | runtime support | |
+| NCL | 6.0 | NCL/6.0 | compiler/intel/13 | application | utility | A library of graphics utilites from the Natl. Center for Atmospheric Research. |
+| NCL | 6.1 | NCL/6.1 | None | application | utility | A library of graphics utilites from the Natl. Center for Atmospheric Research. |
+| NCL | 6.3 | NCL/6.3 | None | application | utility | A library of graphics utilites from the Natl. Center for Atmospheric Research. |
+| NCL | 6.4 | NCL/6.4 | None | application | utility | A library of graphics utilites from the Natl. Center for Atmospheric Research. |
+| NCO | 4.3 | NCO/4.3 | compiler/gcc/4.7 compiler/gcc/4.8 compiler/intel/12 compiler/intel/13 compiler/pgi/12 compiler/pgi/13 | library | runtime support | |
+| NCO | 4.4 | NCO/4.4 | compiler/gcc/4.7 compiler/gcc/4.8 compiler/intel/12 compiler/intel/13 compiler/pgi/12 compiler/pgi/13 | library | runtime support | |
+| NCO | 4.4.6 | NCO/4.4 | compiler/intel/15 compiler/intel/16 compiler/pgi/15 | library | runtime support | |
+| NCO | 4.5.5 | NCO/4.5 | compiler/intel/15 | library | runtime support | |
+| NCO | 4.6.6 | NCO/4.6 | compiler/intel/15 compiler/pgi/12 compiler/pgi/13 compiler/pgi/14 compiler/pgi/15 | library | runtime support | |
+| netcdf | 4.1 | netcdf/4.1 | compiler/intel/13 | library | runtime support | |
+| netcdf | 4.2 | netcdf/4.2 | compiler/gcc/4.7 compiler/gcc/4.8 compiler/intel/12 compiler/intel/13 compiler/pgi/12 compiler/pgi/13 compiler/pgi/14 compiler/pgi/15 | library | runtime support | |
+| netcdf | 4.3 | netcdf/4.3 | compiler/gcc/4.7 compiler/gcc/4.8 compiler/intel/12 compiler/intel/13 compiler/pgi/12 compiler/pgi/13 compiler/pgi/14 compiler/pgi/15 | library | runtime support | |
+| netcdf | 4.4 | netcdf/4.4 | compiler/gcc/4.9 | library | runtime support | |
+| netcdf | 4.4.0 | netcdf/4.4 | compiler/intel/13 compiler/intel/15 compiler/intel/16 compiler/pgi/12 compiler/pgi/13 compiler/pgi/14 compiler/pgi/15 | library | runtime support | |
+| netsurfp | 1.0c | netsurfp/1.0 | None | application | computational biology | NetSurfP predicts the surface accessibility and secondary structure of amino acids in an amino acid sequence. The method also simultaneously predicts the reliability for each prediction, in the form of a Z-score. The Z-score is related to the surface prediction, and not the secondary structure. |
+| NUWRF | NUWRF | NUWRF/intel | None | library | runtime support | |
+| nwchem | 6.3 | nwchem/6.3 | compiler/intel/13:openmpi/1.6 | library | runtime support | |
+| nwchem | 6.5 | nwchem/6.5 | compiler/intel/13:openmpi/1.8 | library | runtime support | |
+| nwchem | 6.6 | nwchem/6.6 | compiler/intel/13:openmpi/1.8 | library | runtime support | |
+| oases | 0.2.09 | oases/0.2 | compiler/gcc/6.1 | application | computational biology | Oases is de novo transcriptome assembler based on the Velvet genome assembler core. |
+| octopus | 5.0 | octopus/5.0 | compiler/intel/13:openmpi/1.10 | library | runtime support | |
+| openbugs | 3.2 | openbugs/3.2 | None | application | statistics | BUGS is a software package for performing Bayesian inference Using Gibbs Sampling. |
+| opencl | 1.2 | opencl/1.2 | None | library | unknown | This runtime software package adds OpenCL CPU device support on systems with Intel Core and Intel Xeon processors. |
+| opencv | 2.4.11 | opencv/2.4 | None | library | unknown | If the library finds Intel's Integrated Performance Primitives on the system, it will use these proprietary optimized routines to accelerate itself. |
+| opencv | 3.1.0 | opencv/3.1 | None | library | unknown | If the library finds Intel's Integrated Performance Primitives on the system, it will use these proprietary optimized routines to accelerate itself. |
+| openmpi | 1.10.2 | openmpi/1.10 | compiler/gcc/4.7 compiler/gcc/4.8 compiler/gcc/4.9 compiler/gcc/5.4 compiler/gcc/6.1 compiler/intel/12 compiler/intel/13 compiler/intel/15 compiler/intel/16 compiler/pgi/12 compiler/pgi/13 compiler/pgi/14 compiler/pgi/15 | library | runtime support | |
+| openmpi | 1.6 | openmpi/1.6 | compiler/gcc/4.7 compiler/gcc/4.8 compiler/gcc/4.9 compiler/intel/12 compiler/intel/13 compiler/intel/15 compiler/pgi/12 compiler/pgi/13 compiler/pgi/14 compiler/pgi/15 | library | runtime support | |
+| openmpi | 1.8 | openmpi/1.8 | compiler/gcc/4.7 compiler/gcc/4.8 compiler/gcc/4.9 compiler/gcc/5.4 compiler/intel/12 compiler/intel/13 compiler/intel/15 compiler/pgi/12 compiler/pgi/13 compiler/pgi/14 compiler/pgi/15 | library | runtime support | |
+| openmpi | 2.0 | openmpi/2.0 | compiler/intel/12 compiler/intel/13 compiler/intel/15 compiler/intel/16 compiler/pgi/12 compiler/pgi/13 compiler/pgi/14 compiler/pgi/15 | library | runtime support | |
+| openmpi | 2.0.1 | openmpi/2.0 | compiler/gcc/4.7 compiler/gcc/4.8 compiler/gcc/4.9 compiler/gcc/5.4 compiler/gcc/6.1 | library | runtime support | |
+| openmpi | 2.1 | openmpi/2.1 | compiler/intel/12 compiler/intel/13 compiler/intel/15 compiler/intel/16 compiler/pgi/12 compiler/pgi/13 compiler/pgi/14 compiler/pgi/15 | library | runtime support | |
+| openmpi | 2.1.1 | openmpi/2.1 | compiler/gcc/4.7 compiler/gcc/4.8 compiler/gcc/4.9 compiler/gcc/5.4 compiler/gcc/6.1 | library | runtime support | |
+| openmx | 3.7 | openmx/3.7 | compiler/intel/13:openmpi/1.8 | library | runtime support | |
+| openmx | 3.8 | openmx/3.8 | compiler/intel/13:openmpi/1.8 | library | runtime support | |
+| p7zip | 16.02 | p7zip/16.02 | None | application | compression | p7zip is a port of 7za.exe for POSIX systems. |
+| pandaseq | 2.9 | pandaseq/2.9 | compiler/gcc/4.9 | application | bioinforomatics | PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence. |
+| parsinsert | 1.04 | parsinsert/1.04 | None | application | computational biology | ParsInsert efficiently produces both a phylogenetic tree and taxonomic classification for sequences for microbial community sequence analysis. This is a C++ implementation of the Parsimonious Insertion algorithm |
+| pbh5tools | 0.8.0 | pbh5tools/0.8 | None | application | computational biology | pbh5tools -- tools for manipulating HDF5 files produced by Pacific Biosciences. Specifically, this package provides functionality for manipulating and extracting data from "cmp.h5" and "bas.h5" files. |
+| pblat | 2.0 | pblat/2.0 | None | application | computational biology | |
+| peridigm | 1.5 | peridigm/1.5 | compiler/gcc/4.9:openmpi/1.10 | library | runtime support | |
+| perl-mongodb | 1.2.2 | perl-mongodb/1.2 | None | application | Utility | This is the official Perl driver for MongoDB. |
+| pesmf | 5.2.0rp3 | pesmf/5.2 | compiler/intel/13:openmpi/1.6 | library | runtime support | |
+| petsc | 3.6 | petsc/3.6 | compiler/gcc/6.1:openmpi/2.0 | library | runtime support | |
+| petsc | 3.9 | petsc/3.9 | compiler/gcc/6.1:openmpi/2.0 | library | runtime support | |
+| phdf5 | 1.8 | phdf5/1.8 | compiler/gcc/4.8:openmpi/1.6 | library | runtime support | |
+| phdf5 | 1.8.15 | phdf5/1.8 | compiler/gcc/4.7:openmpi/1.8 compiler/gcc/4.8:openmpi/1.8 compiler/gcc/4.9:openmpi/1.10 compiler/intel/15:openmpi/1.10 compiler/pgi/12:openmpi/1.8 compiler/pgi/13:openmpi/1.8 compiler/pgi/14:openmpi/1.8 compiler/pgi/15:openmpi/1.8 | library | runtime support | |
+| phobius | 1.01 | phobius/1.01 | None | application | computational biology | Phobius is a combined transmembrane topology and signal peptide predictor. |
+| phonopy | 1.11.12 | phonopy/1.11 | None | library | runtime support | |
+| phrap | 0.990329 | phrap/0.9 | compiler/gcc/4.8 | application | computational biology | Phrap is a program for assembling shotgun DNA sequence data. Cross\_match is a general purpose utility for comparing any two DNA sequence sets using a 'banded' version of swat. Swat is a program for searching one or more DNA or protein query sequences, or a query profile, against a sequence database, using an efficient implementation of the Smith-Waterman or Needleman-Wunsch algorithms with linear (affine) gap penalties. |
+| phylip | 3.696 | phylip/3.696 | compiler/gcc/4.9 | application | computational biology | PHYLIP (the PHYLogeny Inference Package) is a package of programs for inferring phylogenies (evolutionary trees). |
+| phylip | 3.697 | phylip/3.6 | None | library | runtime support | |
+| picard | 1.139 | picard/1.1 | None | application | computational biology | A set of Java command line tools for manipulating high-throughput sequencing data (HTS) data and formats. |
+| picrust | 1.1.0 | picrust/1.1 | None | application | metagenomic | The PICRUSt project aims to support prediction of the unobserved character states in a community of organisms from phylogenetic information about the organisms in that community. |
+| pnetcdf | 4.2 | pnetcdf/4.2 | compiler/gcc/4.8:openmpi/1.6 | library | runtime support | |
+| pnetcdf | 4.4 | pnetcdf/4.4 | compiler/gcc/4.9:openmpi/1.10 | library | runtime support | |
+| PNG | 1.2.50 | PNG/1.2 | compiler/intel/13 | library | runtime support | |
+| pplacer | 1.1 | pplacer/1.1 | None | application | computational biology | Pplacer places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment. |
+| primer3 | 2.3.7 | primer3/2.3 | None | application | computational biology | Primer3 picks primers for PCR reactions |
+| prinseq-lite | 0.20.4 | prinseq-lite/0.20 | None | application | computational biology | PRINSEQ can be used to filter, reformat, or trim your genomic and metagenomic sequence data. |
+| prodigal | 2.60 | prodigal/2.60 | None | application | computational biology | Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee. |
+| prohlatype | 0.9.0 | prohlatype/0.9 | None | application | Computational Biology | This project provides a set of tools to calculate the full posterior distribution of HLA types given read data. |
+| proj | 4.9 | proj/4.9 | compiler/gcc/4.9 | library | runtime support | |
+| pymagic | 0.1 | pymagic/0.1 | None | application | computational biology | MAGIC: A diffusion-based imputation method reveals gene-gene interactions in single-cell RNA-sequencing data. |
+| pymeteo | 0.5 | pymeteo/0.5 | None | application | geoscience | General meteorological routines, skew-T/log-p plotting and working with CM1 model data. |
+| python | 3.3 | python/3.3 | None | application | system | |
+| python-openstackclient | 2.1.0 | python-openstackclient/2.1 | None | application | Utility | OpenStackClient (aka OSC) is a command-line client for OpenStack that brings the command set for Compute, Identity, Image, Object Store and Block Storage APIs together in a single shell with a uniform command structure. |
+| pytorch/py36 | 0.3.0 | pytorch/py36/0.3 | None | application | Deep Learning | PyTorch is a deep learning framework that puts Python first. |
+| qctool | 1.4 | qctool/1.4 | None | application | computational biology | QCTOOL is a command-line utility program for basic quality control of gwas datasets. |
+| qiime | 1.8 | qiime/1.8 | None | application | computational biology | QIIME is an open source software package for comparison and analysis of microbial communities, primarily based on high-throughput amplicon sequencing data (such as SSU rRNA) generated on a variety of platforms, but also supporting analysis of other types of data (such as shotgun metagenomic data). |
+| qiime | 1.9 | qiime/1.9 | None | application | computational biology | QIIME is an open source software package for comparison and analysis of microbial communities, primarily based on high-throughput amplicon sequencing data (such as SSU rRNA) generated on a variety of platforms, but also supporting analysis of other types of data (such as shotgun metagenomic data). |
+| qiime | 2017.9 | qiime/2.0 | None | application | computational biology | QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency. |
+| qiime2 | 2017.9 | qiime2/2017.9 | None | application | computational biology | QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency. |
+| qiime2 | 2018.2 | qiime2/2018.2 | None | application | computational biology | QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency. |
+| quast | 4.1 | quast/4.1 | None | application | computational biology | QUAST. the QUality ASsessment Tool for genome assemblies. |
+| R | 3.0 | R/3.0 | compiler/intel/12 compiler/intel/13 None | library | runtime support | |
+| R | 3.1 | R/3.1 | None | library | runtime support | |
+| R | 3.2 | R/3.2 | compiler/intel/15 None | library | runtime support | |
+| R | 3.3 | R/3.3 | None | library | runtime support | |
+| RAPSearch2 | 2.19 | RAPSearch2/2.19 | None | application | computational biology | RAPSearch2 is a tool for fast protein similarity searches. |
+| ray | 2.3 | ray/2.3 | compiler/gcc/4.8:openmpi/1.6 compiler/gcc/4.8:openmpi/1.8 | application | computational biology | Ray -- Parallel genome assemblies for parallel DNA sequencing. |
+| repeatmasker | 4.0 | repeatmasker/4.0 | None | application | computational biology | RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. |
+| rmblast | 2.28 | rmblast/2.28 | compiler/gcc/4.8 | application | computational biology | RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST suite. The primary difference between this distribution and the NCBI distribution is the addition of a new program 'rmblastn' for use with RepeatMasker and RepeatModeler. |
+| rnammer | 1.2 | rnammer/1.2 | None | application | computational biology | RNAmmer predicts 5s/8s, 16s/18s, and 23s/28s ribosomal RNA in full genome sequences. |
+| root | 6.06.08 | root/6.06 | compiler/gcc/4.9 | application | big data | It provides all the functionalities needed to deal with big data processing, statistical analysis, visualisation and storage. |
+| rosetta | 3.8 | rosetta/3.8 | compiler/gcc/4.9:openmpi/2.0 | application | computational biology | The Rosetta software suite includes algorithms for computational modeling and analysis of protein structures. It has enabled notable scientific advances in computational biology, including de novo protein design, enzyme design, ligand docking, and structure prediction of biological macromolecules and macromolecular complexes. |
+| r-scimpute | 0.0.5 | r-scimpute/0.0.5 | None | application | biology | scImpute is accurate and robust imputation of single-cell RNA sequencing data. |
+| rsem | 1.2 | rsem/1.2 | None | application | computational biology | RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. |
+| ruby | 2.1 | ruby/2.1 | None | application | system | |
+| saga | 2.1 | saga/2.1 | compiler/gcc/4.9 | application | GIS | SAGA: System for Automated Geoscientific Analyses. |
+| saga | 2.2 | saga/2.2 | compiler/gcc/4.9 | application | GIS | SAGA: System for Automated Geoscientific Analyses. |
+| saga | 2.3 | saga/2.3 | compiler/gcc/4.9 | application | GIS | SAGA: System for Automated Geoscientific Analyses. |
+| sage | 6.3 | sage/6.3 | None | application | mathematics | 'Sage is a free open-source mathematics software system licensed under the GPL. It builds on top of many existing open-source packages: NumPy, SciPy, matplotlib, Sympy, Maxima, GAP, FLINT, R and many more.' Mission: 'Creating a viable free open source alternative to Magma, Maple, Mathematica and Matlab.' |
+| sage | 8.0 | sage/8.0 | compiler/gcc/5.4 | application | mathematics | 'Sage is a free open-source mathematics software system licensed under the GPL. It builds on top of many existing open-source packages: NumPy, SciPy, matplotlib, Sympy, Maxima, GAP, FLINT, R and many more.' Mission: 'Creating a viable free open source alternative to Magma, Maple, Mathematica and Matlab.' |
+| samtools | 0.1 | samtools/0.1 | None | application | computational biology | SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. |
+| samtools | 1.1 | samtools/1.1 | compiler/gcc/4.8 | application | computational biology | SAM Tools - a generic tool for the sam format alignments. |
+| samtools | 1.2 | samtools/1.2 | compiler/gcc/4.8 | application | computational biology | SAM Tools - a generic tool for the sam format alignments. |
+| samtools | 1.3.1 | samtools/1.3 | None | application | computational biology | SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. |
+| scan-for-matches | 1.0 | scan-for-matches/1.0 | None | application | computational biology | scan\_for\_matches is a utility written in C for locating patterns in DNA or protein FASTA files. |
+| scip | 4.0.0 | scip/4.0 | None | application | constraint integer programming | SCIP is currently one of the fastest non-commercial solvers for mixed integer programming (MIP) and mixed integer nonlinear programming (MINLP). |
+| sepp | 1.0 | sepp/1.0 | None | library | runtime support | |
+| settarg | settarg | settarg/settarg | None | application | unknown | |
+| sff2fastq | 0.9 | sff2fastq/0.9 | None | application | computational biology | sff2fast extracts 454 Genome Sequencer reads from a SFF file and converts them into a FASTQ formatted output |
+| shengbte | 1.1.1 | shengbte/1.1 | compiler/gcc/4.9:openmpi/1.10 | library | runtime support | |
+| shrimp | 2.2 | shrimp/2.2 | None | application | computational biology | SHRiMP is a software package for aligning genomic reads against a target genome. |
+| shtns | 2.8 | shtns/2.6 | compiler/intel/15 | application | math | |
+| sickle | 1.2 | sickle/1.210 | None | application | computational biology | A windowed adaptive trimming tool for FASTQ files using quality |
+| siesta | 4.1.3 | siesta/4.1 | compiler/gcc/4.9:openmpi/1.10 compiler/intel/13:openmpi/1.8 compiler/intel/15:openmpi/1.10 | library | runtime support | |
+| signalp | 4.1 | signalp/4.1 | None | application | computational biology | signalp predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive bacteria, Gram-negative bacteria, and eukaryotes. |
+| simrna | 3.20 | simrna/3.20 | None | application | computational biology | SimRNA is a tool for simulations of RNA conformational dynamics |
+| smrtlink | 5.0.1 | smrtlink/5.0 | None | application | biology | PacBio’s open-source SMRT Analysis software suite is designed for use with Single Molecule, Real-Time (SMRT) Sequencing data. |
+| smrtlink | 5.1.0 | smrtlink/5.1 | None | application | biology | PacBio’s open-source SMRT Analysis software suite is designed for use with Single Molecule, Real-Time (SMRT) Sequencing data. |
+| snap | 2013-11-29 | snap/2013-11-29 | None | application | computational biology | SNAP - (Semi-HMM-based Nucleic Acid Parser) gene prediction tool. |
+| snp-pipeline | 0.6 | snp-pipeline/0.6 | None | application | computational biology | SNP Pipeline is a pipeline for the production of SNP matrices from sequence data used in the phylogenetic analysis of pathogenic organisms sequenced from samples of interest to food safety. |
+| snptest | 2.5.2 | snptest/2.5 | None | application | computational biology | SNPTEST is a program for the analysis of single SNP association in genome-wide studies. |
+| soapdenovo2 | r240 | soapdenovo2/r240 | None | application | computational biology | soapdenovo2 - novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes |
+| sonnet-gpu | 1.19 | sonnet-gpu/py27/1.19 | None None None | application | machine learning | Sonnet is a library built on top of TensorFlow for building complex neural networks. |
+| sonnet-gpu | 1.23 | sonnet-gpu/py27/1.23 | None None None | application | machine learning | Sonnet is a library built on top of TensorFlow for building complex neural networks. |
+| spglib | 1.9.9 | spglib/1.9 | compiler/gcc/4.9 | library | runtime support | |
+| spider | 2.0 | spider/2.0 | None | application | computational biology | Sequence-based Prediction of Local and Nonlocal Structural Features for Proteins. |
+| spp | 1.11 | spp/1.11 | None | application | computational biology | ChIP-seq peak caller |
+| spp | 1.13 | spp/1.13 | None | application | computational biology | ChIP-seq peak caller |
+| SRAtoolkit | 2.8 | SRAtoolkit/2.8 | None | application | computational biology | SRA Toolkit |
+| SRAtoolkit | 2.9 | SRAtoolkit/2.9 | None | application | computational biology | The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. |
+| star | 2.5.3a | star/2.5 | compiler/gcc/4.9 | application | biology | Spliced Transcripts Alignment to a Reference |
+| starccm | 10.01.010 | starccm/10.06 | None | library | runtime support | |
+| starccm | 9.01.011 | starccm/9.06 | None | library | runtime support | |
+| StringTie | 1.3.0 | StringTie/1.3 | None | application | computational biology | StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. |
+| structure | 2.3 | structure/2.3 | None | application | computational biology | The program structure is a free software package for using multi-locus genotype data to investigate population structure. |
+| subread | 1.4 | subread/1.4 | None | application | computational biology | The Subread package is developed in The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia. It consists of a suite of programs for processing next-gen sequencing data. |
+| szip | 2.1 | szip/2.1 | compiler/gcc/4.7 compiler/gcc/4.8 compiler/gcc/4.9 compiler/intel/12 compiler/intel/13 compiler/intel/15 compiler/intel/16 compiler/pgi/12 compiler/pgi/13 compiler/pgi/14 compiler/pgi/15 None | library | runtime support | |
+| tabix | 0.2 | tabix/0.2 | None | application | computational biology | Tabix indexes a TAB-delimited genome position file in.tab.bgz and creates an index file |
+| tagcleaner | 0.16 | tagcleaner/0.16 | None | application | computational biology | The TagCleaner tool can be used to automatically detect and efficiently remove tag sequences (e.g. WTA tags) from genomic and metagenomic datasets. It is easily configurable and provides a user-friendly interface. |
+| tassel | 3.0 | tassel/3.0 | None | application | computational biology | While TASSEL has changed considerably since its initial public release in 2001, its primary function continues to be providing tools to investigate the relationship between phenotypes and genotypes1. As indicated by its title – Trait Analysis by aSSociation, Evolution and Linkage – TASSEL has multiple functions, including association study, evaluating evolutionary relationships, analysis of linkage disequilibrium, principal component analysis, cluster analysis, missing data imputation and data visualization. |
+| tassel | 4.0 | tassel/4.0 | None | application | computational biology | While TASSEL has changed considerably since its initial public release in 2001, its primary function continues to be providing tools to investigate the relationship between phenotypes and genotypes1. As indicated by its title – Trait Analysis by aSSociation, Evolution and Linkage – TASSEL has multiple functions, including association study, evaluating evolutionary relationships, analysis of linkage disequilibrium, principal component analysis, cluster analysis, missing data imputation and data visualization. |
+| tassel | 5.1 | tassel/5.1 | None | application | computational biology | While TASSEL has changed considerably since its initial public release in 2001, its primary function continues to be providing tools to investigate the relationship between phenotypes and genotypes1. As indicated by its title – Trait Analysis by aSSociation, Evolution and Linkage – TASSEL has multiple functions, including association study, evaluating evolutionary relationships, analysis of linkage disequilibrium, principal component analysis, cluster analysis, missing data imputation and data visualization. |
+| taxypro | 1.0 | taxypro/1.0 | None | application | mixture modeling for taxonomic analysis of metagenomes | |
+| taxytoolbox | 1.0 | taxytoolbox/1.0 | None | application | mixture modeling for taxonomic analysis of metagenomes | |
+| tensorflow | 0.12.1 | tensorflow/py35/0.12 | None None | application | machine learning | TensorFlow is an open source software library for numerical computation using data flow graphs. |
+| tensorflow | 1.0.0 | tensorflow/py35/1.0 | None None | application | machine learning | TensorFlow is an open source software library for numerical computation using data flow graphs. |
+| tensorflow | 1.3.1 | tensorflow/py35/1.3 | None None None | application | machine learning | TensorFlow is an open source software library for numerical computation using data flow graphs. |
+| tensorflow | 1.4.0 | tensorflow/py36/1.4 | None None None | application | machine learning | TensorFlow is an open source software library for numerical computation using data flow graphs. |
+| tensorflow | 1.5.0 | tensorflow/py35/1.5 | None None None | application | machine learning | TensorFlow is an open source software library for numerical computation using data flow graphs. |
+| tensorflow | 1.7.0 | tensorflow/py35/1.7 | None None None | application | machine learning | TensorFlow is an open source software library for numerical computation using data flow graphs. |
+| tensorflow-gpu | 1.5.0 | tensorflow-gpu/py35/1.5 | None None None | application | machine learning | TensorFlow is an open source software library for numerical computation using data flow graphs. |
+| tensorflow-gpu | 1.7.0 | tensorflow-gpu/py36/1.7 | None None None | application | machine learning | TensorFlow is an open source software library for numerical computation using data flow graphs. |
+| tmhmm | 2.0c | tmhmm/2.0c | None | application | computational biology | TMHMM 2.0 predicts transmembrane helices in proteins. |
+| tophat | 2.0 | tophat/2.0 | None | application | computational biology | TopHat2 is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons. |
+| tophat | 2.1.0 | tophat/2.1 | None | application | computational biology | TopHat2 is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons. |
+| transdecoder | 2.0.1 | transdecoder/2.0 | None | application | computational biology | TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. |
+| transrate | 0.1 | transrate/0.1 | None | application | life sciences | transrate - Quality assessment and comparison of transcriptome assemblies |
+| treemix | 1.12 | treemix/1.12 | None | application | computational biology | TreeMix is a method for inferring the patterns of population splits and mixtures in the history of a set of populations. |
+| trf | 4.07b | trf/4.0 | None | application | computational biology | Tandem Repeats Finder is a program to locate and display tandem repeats in DNA sequences. |
+| tricubic | 1.0 | tricubic/1.0 | compiler/gcc/4.9 | library | runtime support | |
+| trilinos | 12.6 | trilinos/12.6 | compiler/gcc/4.9:openmpi/1.10 | library | runtime support | |
+| trim\_galore | 0.4.0 | trim\_galore/0.4 | None | application | computational biology | Trim sequences |
+| TrimGalore | 0.4.5 | TrimGalore/0.4 | None | library | runtime support | |
+| trimmomatic | 0.33 | trimmomatic/0.33 | None | application | computational biology | Trimmomatic: A flexible read trimming tool for Illumina NGS data. |
+| trinity | 2.0 | trinity/2.0 | compiler/gcc/4.8 | application | computational biology | Package for RNA-Seq de novo Assembly |
+| trinity | 2.1 | trinity/2.1 | compiler/gcc/4.8 | application | computational biology | Package for RNA-Seq de novo Assembly |
+| trinity | r2013-11-10 | trinity/r2013-11-10 | None | application | computational biology | Package for RNA-Seq de novo Assembly |
+| trinity | r2014-04-13p1 | trinity/r2014-04-13p1 | None | application | computational biology | Package for RNA-Seq de novo Assembly |
+| trinotate | 2.0.2 | trinotate/2.0 | None | application | computational biology | Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. |
+| trinotate | r2013-11-10 | trinotate/r2013-11-10 | None | application | computational biology | Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. |
+| twobittofa | 1.0 | twobittofa/1.0 | None | application | unknown | This is a bioinformatics, freely downloadable command-line software (linux.x86\_64) provided by the UCSC |
+| udunits2 | 2.1 | udunits2/2.1 | compiler/gcc/4.7 compiler/gcc/4.8 compiler/intel/12 compiler/intel/13 compiler/pgi/12 compiler/pgi/13 compiler/pgi/14 compiler/pgi/15 | library | runtime support | |
+| udunits2 | 2.2 | udunits2/2.2 | compiler/intel/13 compiler/intel/15 compiler/intel/16 compiler/pgi/12 compiler/pgi/13 compiler/pgi/14 compiler/pgi/15 | library | runtime support | |
+| upcr | 2.20 | upcr/2.20 | compiler/gcc/4.9:openmpi/1.8 | application | compiler | |
+| upcr | 2.24 | upcr/2.24 | compiler/gcc/5.4:openmpi/2.0 | application | compiler | |
+| usearch | 5.2 | usearch/5.2 | None | application | computational biology | USEARCH is a unique sequence analysis tool with thousands of users world-wide. USEARCH offers search and clustering algorithms that are often orders of magnitude faster than BLAST. |
+| usearch | 6.1 | usearch/6.1 | None | application | computational biology | USEARCH is a unique sequence analysis tool with thousands of users world-wide. USEARCH offers search and clustering algorithms that are often orders of magnitude faster than BLAST. |
+| usearch | 7.0 | usearch/7.0 | None | application | computational biology | USEARCH is a unique sequence analysis tool with thousands of users world-wide. USEARCH offers search and clustering algorithms that are often orders of magnitude faster than BLAST. |
+| varscan | 2.3 | varscan/2.3 | None | application | computational biology | VarScan is a platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM, Roche/454, and similar instruments. |
+| vasp | 5.4 | vasp/5.4sol | compiler/intel/13:openmpi/1.8 compiler/intel/15:openmpi/2.1 | library | runtime support | |
+| vasp | 5.4.4 | vasp/5.4.4 | compiler/intel/15:openmpi/2.1 | library | runtime support | |
+| vcftools | 0.1 | vcftools/0.1 | None | application | computational biology | VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files. |
+| velvet | 1.2 | velvet/1.2 | None | application | computational biology | Velvet - Sequence assembler for very short reads |
+| virema | 0.6 | virema/0.6 | None | application | computational biology | |
+| wevote | 1.8 | wevote/1.8 | None | library | runtime support | |
+| wgrib2 | 2.0.6 | wgrib2/2.0 | None | application | file processing | wgrib2 is more like four drawers of kitchen utensils as well as the microwave and blender. |
+| WRF | WRF | WRF/1.0 | compiler/intel/15:openmpi/1.10 compiler/intel/16:openmpi/1.10 compiler/pgi/15:openmpi/1.10 compiler/pgi/15:openmpi/1.10 None None None | library | runtime support | |
+| xpclr | 1.0 | xpclr/1.0 | None | application | computational biology | detecting selective sweeps via the differentiation of two populations |
+| xzutils | 5.2 | xzutils/5.2 | None | library | runtime support | |
+| zlib | 1.2 | zlib/1.2 | compiler/gcc/4.7 compiler/gcc/4.8 compiler/gcc/4.9 compiler/intel/12 compiler/intel/13 compiler/intel/15 compiler/intel/16 compiler/pgi/12 compiler/pgi/13 compiler/pgi/14 compiler/pgi/15 None | library | runtime support | |
+
+
+
+| Name | Version | Module Name | Prerequisites | Type | Domain | Description |
+|-----------------------|--------------|--------------------------------|----------------|-------------|---------------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| abayesqr | 1.0 | abayesqr/1.0 | None | application | high-throughput sequencing data | aBayesQR is a viral quasispecies reconstruction algorithm that employs a maximum-likelihood framework to infer individual sequences in a mixture from high-throughput sequencing data. |
+| afni | 18.2.06 | afni/18.2 | None | application | MRI | AFNI is a suite of programs for looking at and analyzing 3D brain images. |
+| afterqc | 0.9.6 | afterqc/0.9 | None | application | package | Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data. AfterQC can simply go through all fastq files in a folder and then output three folders: good, bad and QC folders, which contains good reads, bad reads and the QC results of each fastq file/pair. Currently it supports processing data from HiSeq 2000/2500/3000/4000, Nextseq 500/550, MiniSeq...and other Illumina 1.8 or newer formats. |
+| agfusion | 1.0 | agfusion/1.0 | None | application | Biology | AGFusion is a python package for annotating gene fusions from the human or mouse genomes. |
+| allinea | 18.0 | allinea/18.0 | None | application | Utility | |
+| allinea | 18.2 | allinea/18.2 | None | application | Utility | |
+| allinea | 4.2 | allinea/4.2 | None | application | Utility | |
+| allinea | 5.0 | allinea/5.0 | None | application | Utility | |
+| allinea | 5.1 | allinea/5.1 | None | application | Utility | |
+| allinea | 6.0 | allinea/6.0 | None | application | Utility | |
+| allinea | 6.1 | allinea/6.1 | None | application | Utility | |
+| allinea | 7.0 | allinea/7.0 | None | application | Utility | |
+| ant | 1.10.1 | ant/1.10 | None | library | java | Java build tool |
+| ant | 1.9.9 | ant/1.9 | None | library | java | Java build tool |
+| apkid | 1.0.0 | apkid/1.0 | None | application | Malware | APKiD is Android Application Identifier for Packers, Protectors, Obfuscators and Oddities - PEiD for Android. |
+| aria2 | 1.23.0 | aria2/1.23 | None | application | tool | aria2 is a lightweight multi-protocol & multi-source command-line download utility. |
+| aspera-cli | 3.7.7 | aspera-cli/3.7 | None | application | system | IBM Aspera Command-Line Interface (the Aspera CLI) is a collection of Aspera tools for performing high-speed, secure data transfers from the command line. |
+| augustus | 3.2.3 | augustus/3.2 | None | application | computational biology | AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke and Oliver Keller. It can be used as an ab initio program, which means it bases its prediction purely on the sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources such as EST, MS/MS, protein alignments and synthenic genomic alignments. |
+| augustus | 3.3 | augustus/3.3 | None | application | computational biology | AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke and Oliver Keller. It can be used as an ab initio program, which means it bases its prediction purely on the sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources such as EST, MS/MS, protein alignments and synthenic genomic alignments. |
+| autoconf | 2.69 | autoconf/2.69 | None | application | Utilities | Extensible M4 macros that produce shell scripts to configure software source code packages. |
+| autodock | 4.2.6 | autodock/4.2 | None | application | Chemistry | AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. |
+| awscli | 1.1.120 | awscli/1.11 | None | application | utility | The AWS CLI is an open source tool built on top of the AWS SDK for Python (Boto) that provides commands for interacting with AWS services. |
+| bam-readcount | 0.8 | bam-readcount/0.8 | None | application | computational biology | The purpose of this program is to generate metrics at single nucleotide positions. |
+| bamtools | 2.3.0 | bamtools/2.3 | None | application | computational biology | C++ API & command-line toolkit for working with BAM data |
+| bamtools | 2.4.1 | bamtools/2.4 | None | application | computational biology | C++ API & command-line toolkit for working with BAM data |
+| bbmap | 37.17 | bbmap/37.17 | None | application | computational biology | BBMap is a splice-aware global aligner for DNA and RNA sequencing reads. |
+| bbmap | 38.06 | bbmap/38.06 | None | application | computational biology | BBMap is a splice-aware global aligner for DNA and RNA sequencing reads. |
+| bcftools | 1.3.1 | bcftools/1.3 | None | application | computational biology | BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations. |
+| bcftools | 1.8 | bcftools/1.8 | None | application | computational biology | BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations. |
+| beagle | 4.1\_21Jan17 | beagle/4.1 | None | application | Biology | Beagle is a software package that performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection. |
+| beast | 1.8 | beast/1.8 | None | application | biology | BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC. |
+| beast2 | 2.4 | beast2/2.4 | None | application | biology | BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences. |
+| bedops | 2.4.35 | bedops/2.4 | None | application | computational biology | BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale. |
+| bedtools | 2.24.0 | bedtools/2.24 | None | application | computational biology | A powerful toolset for genome arithmetic |
+| bedtools | 2.27.1 | bedtools/2.27 | None | application | computational biology | A powerful toolset for genome arithmetic |
+| beta | 1.0.7 | beta/1.0 | None | application | computational biology | Binding and Expression Target Analysis (BETA) is a software package that integrates ChIP-seq of transcription factors or chromatin regulators with differential gene expression data to infer direct target genes. |
+| binutils | 2.30 | binutils/2.30 | None | application | Utilities | The GNU Binutils are a collection of binary tools. |
+| bioconductor | 3.4 | bioconductor/3.4 | None | application | computational biology | Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. |
+| bioconductor-ballgown | 2.2.0 | bioconductor-ballgown/2.2 | None | application | computational biology | Tools for statistical analysis of assembled transcriptomes, including flexible differential expression analysis, visualization of transcript structures, and matching of assembled transcripts to annotation. |
+| bioconductor-jmosaics | 1.10 | bioconductor-jmosaics/1.10 | None | application | computational biology | Joint analysis of multiple ChIP-Seq data sets. |
+| biodata | 1.0 | biodata/1.0 | None | application | computational biology | Static data resources for bioinformatics/computational biology. |
+| biom-format | 2.1 | biom-format/2.1 | None | application | computational biology | The BIOM file format (canonically pronounced biome) is designed to be a general-use format for representing biological sample by observation contingency tables. BIOM is a recognized standard for the Earth Microbiome Project and is a Genomics Standards Consortium supported project. |
+| bioperl | 1.6.924 | bioperl/1.6.924 | None | application | computational biology | BioPerl - Perl Modules for Biology |
+| biopython | 1.70 | biopython/py36/1.70 | None None None | library | biological computation | Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. |
+| biopython | 1.71 | biopython/py27/1.71 | None None None | library | biological computation | Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. |
+| blast | 2.6.0 | blast/2.6 | None | application | computational biology | NCBI BLAST+ sequence alignment package. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. |
+| blast | 2.7.1 | blast/2.7 | None | application | computational biology | NCBI BLAST+ sequence alignment package. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. |
+| breakdancer | 1.4 | breakdancer/1.4 | None | application | computational biology | BreakDancer is a Perl/C++ package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads. |
+| breakseq2 | 2.2 | breakseq2/2.2 | None | application | computational biology | BreakSeq2: Ultrafast and accurate nucleotide-resolution analysis of structural variants. |
+| bsmap | 2.90 | bsmap/2.90 | None | application | Mapping | BSMAP is a short reads mapping software for bisulfite sequencing reads. |
+| bx-python | 0.8.1 | bx-python/py27/0.8 | None None None | application | computational biology | Tools for manipulating biological data, particularly multiple sequence alignments |
+| canu | 1.7 | canu/1.7 | None | application | computational biology | Canu is a fork of the Celera Assembler, designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION). |
+| ccat | 3.0 | ccat/3.0 | None | application | computational biology | A software package for the analysis of ChIP-seq data with negative control. |
+| clove | 0.17 | clove/0.17 | None | application | computational biology | CLOVE: Classification of genomic fusions into structural variation events. |
+| clustalw | 2.1 | clustalw/2.1 | None | application | computational biology | ClustalW2 is a multiple sequence alignment tool for the alignment of DNA or protein sequences. |
+| cmake | 2.8.10.2 | cmake/2.8 | None | application | system | CMake is an extensible, open-source system that manages the build process |
+| cmake | 3.10.3 | cmake/3.10 | None | application | system | CMake is an extensible, open-source system that manages the build process |
+| cmake | 3.11.3 | cmake/3.11 | None | application | system | CMake is an extensible, open-source system that manages the build process |
+| cmake | 3.5.0 | cmake/3.5 | None | application | system | CMake is an extensible, open-source system that manages the build process |
+| cmake | 3.7.1 | cmake/3.7 | None | application | system | CMake is an extensible, open-source system that manages the build process |
+| codonw | 1.4.4 | codonw/1.4 | None | application | computational biology | CodonW is a programme designed to simplify the Multivariate analysis (correspondence analysis) of codon and amino acid usage. |
+| connectome-workbench | 1.3.1 | connectome-workbench/1.3 | None | application | neuroimaging | Connectome Workbench is an open source, freely available visualization and discovery tool used to map neuroimaging data, especially data generated by the Human Connectome Project |
+| cutadapt | 1.13 | cutadapt/1.13 | None | application | NGS data | Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. |
+| cutadapt | 1.4 | cutadapt/1.4 | None | application | computational biology | Cutadapt removes adapter sequences from DNA high-throughput sequencing data. |
+| deap | 1.0 | deap/1.0 | None | application | computer science | DEAP is a novel evolutionary computation framework for rapid prototyping and testing of ideas. |
+| deeptools | 2.5.4 | deeptools/2.5 | None | application | computational biology | |
+| detectron/py27 | 2018.09.11 | detectron/py27/2018.09.11 | None | application | object detection | FAIR's research platform for object detection research, implementing popular algorithms like Mask R-CNN and RetinaNet. |
+| eigen | 3.3.3 | eigen/3.3 | None | library | C++ | C++ template library for linear algebra |
+| entrez-direct | 10.0 | entrez-direct/10.0 | None | application | Entrez | Entrez Direct (EDirect) is an advanced method for accessing the NCBI's set of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window. Functions take search terms from command-line arguments. Individual operations are combined to build multi-step queries. Record retrieval and formatting normally complete the process. |
+| eqtlbma | 1.3 | eqtlbma/1.3 | None | application | biology | Package to detect eQTLs jointly in multiple subgroups (e.g. tissues) via Bayesian Model Averaging. |
+| fastqc | 0.11.7 | fastqc/0.11 | None | application | computational biology | fastqc - A Quality Control application for FastQ files |
+| fasttree | 2.1.10 | fasttree/2.1 | None | application | computational biology | FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. |
+| fqtrim | 0.9.7 | fqtrim/0.9 | None | application | computational biology | fqtrim: trimming & filtering of NGS reads. |
+| freebayes | 1.2.0 | freebayes/1.2 | None | application | Biology | Bayesian haplotype-based polymorphism discovery and genotyping |
+| freesurfer | 5.3.0 | freesurfer/5.3 | None | application | computational neuroimaging | An open source software suite for processing and analyzing (human) brain MRI images. |
+| freesurfer | 6.0.0 | freesurfer/6.0 | None | application | computational neuroimaging | An open source software suite for processing and analyzing (human) brain MRI images. |
+| gatk4 | 4.0.4.0 | gatk4/4.0 | None | application | computational biology | GATK4: This toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. |
+| gaussian | 09 RevD | gaussian/09/RevD | None | application | Chemistry | |
+| gaussian | 09 RevE | gaussian/09/RevE | None | application | Chemistry | |
+| gaussian | 16 RevE | gaussian/16/RevA | None | application | Chemistry | |
+| gdcclient | 1.3.0 | gdcclient/1.3 | None | application | genomics | GDC provides a standard client-based mechanism in support of high performance data downloads and submission. |
+| gem | 2.7 | gem/2.7 | None | application | computational biology | GEM: High resolution peak calling and motif discovery for ChIP-seq and ChIP-exo data. |
+| geoparse | 1.0.5 | geoparse/1.0 | None | application | Bioinformatics | Python library to access Gene Expression Omnibus Database (GEO) |
+| ghostscript | 9.20 | ghostscript/9.20 | None | library | runtime support | An interpreter for the PostScript language and for PDF. |
+| ghostscript | 9.22 | ghostscript/9.22 | None | library | runtime support | An interpreter for the PostScript language and for PDF. |
+| git | 2.17.0 | git/2.17 | None | library | tools | distributed version control system |
+| git | 2.7.4 | git/2.7 | None | library | tools | distributed version control system |
+| globus-cli | 1.2.0 | globus-cli/1.2 | None | application | tool | Command line clients provide an interface to Globus services from the shell, and are suited for both interactive use and simple scripting use cases. |
+| glpk | 4.61 | glpk/4.61 | None | application | mathematics | The GLPK (GNU Linear Programming Kit) package is intended for solving large-scale linear programming (LP), mixed integer programming (MIP), and other related problems. It is a set of routines written in ANSI C and organized in the form of a callable library. |
+| gmap | 2015.12.31 | gmap/2015.12.31 | None | application | computational biology | GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and GSNAP: Genomic Short-read Nucleotide Alignment Program. |
+| gmap | 2017.05.08 | gmap/2017.05.08 | None | application | computational biology | GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and GSNAP: Genomic Short-read Nucleotide Alignment Program. |
+| gmap | 2018.03.25 | gmap/2018.03.25 | None | application | computational biology | GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and GSNAP: Genomic Short-read Nucleotide Alignment Program. |
+| gnu-parallel | 20180522 | gnu-parallel/20180522 | None | application | Shell tool | GNU parallel is a shell tool for executing jobs in parallel using one or more computers. |
+| gnuplot | 4.6.0 | gnuplot/4.6 | None | application | unknown | Gnuplot, plotting from command line |
+| gnuplot | 5.2.3 | gnuplot/5.2 | None | application | unknown | Gnuplot, plotting from command line |
+| graphlan | 1.0.0 | graphlan/1.0 | None | application | unknown | GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. It focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation. |
+| graphviz | 2.38.0 | graphviz/2.38 | None | library | unknown | |
+| gtdbtk | 0.1.3 | gtdbtk/0.1 | None | application | computational biology | A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes. |
+| hotspot3d | 0.6.0 | hotspot3d/0.6 | None | application | bioinformatics | This 3D proximity tool can be used to identify mutation hotspots from linear protein sequence and correlate the hotspots with known or potentially interacting domains, mutations, or drugs. Mutation-mutation and mutation-drug clusters can also be identified and viewed. |
+| htseq | 0.5.4p5 | htseq/0.5.4p5 | None | application | computational biology | HTSeq - Analysing high-throughput sequencing data with Python |
+| htseq | 0.6.1p1 | htseq/0.6.1p1 | None | application | computational biology | HTSeq - Analysing high-throughput sequencing data with Python |
+| htseq | 0.9.1 | htseq/0.9 | None | application | computational biology | HTSeq - Analysing high-throughput sequencing data with Python |
+| htslib | 1.7 | htslib/1.7 | None | application | computational biology | HTSlib is an implementation of a unified C library for accessing common file formats. |
+| htstream | e919d21 | htstream/e919d21 | None | application | Bioinformatics | A toolset for high throughput sequence analysis using a streaming approach facilitated by Linux pipes. |
+| imagemagick | 7.0.8\_10 | imagemagick/7.0 | None | application | bitmap | Software suite to create, edit, compose, or convert bitmap images. |
+| impute2 | 2.3.2 | impute2/2.3 | None | application | computational biology | IMPUTE2 is a computer program for phasing observed genotypes and imputing missing genotypes. |
+| iqtree | 1.6.7 | iqtree/1.6 | None | application | computational biology | IQ-TREE creates phylogenetic trees under maximum likelihood with emphasis on speed and accuracy. |
+| jamm | 1.0.7r2 | jamm/1.0.7r2 | None | application | computational biology | JAMM is a peak finder for NGS datasets (ChIP-Seq, ATAC-Seq, DNase-Seq..etc.) that can integrate replicates and assign peak boundaries accurately. |
+| java | 1.6 | java/1.6 | None | application | system | Java JDK. |
+| java | 1.7 | java/1.7 | None | application | system | Java JDK. |
+| java | 1.8 | java/1.8 | None | application | system | Java JDK. |
+| julia | 1.0 | julia/1.0 | None | application | Language | A high-performance dynamic programming language for data science |
+| jvarkit-msa2vcf | 1.0 | jvarkit-msa2vcf/1.0 | None | application | computational biology | Getting a VCF file from a CLUSTAW or a FASTA alignment. |
+| jvarkit-sam2tsv | 1.0 | jvarkit-sam2tsv/1.0 | None | application | computational biology | Prints the SAM alignments as a TAB delimited file. |
+| kalign | 2.0 | kalign/2.0 | None | application | computational biology | Kalign is a fast and accurate multiple sequence alignment algorithm designed to align large numbers of protein sequences. |
+| ksnp | 3.1 | ksnp/3.1 | None | application | computational biology | kSNP identifies the pan-genome SNPs in a set of genome sequences, and estimates phylogenetic trees based upon those SNPs. |
+| lftp | 4.8.3 | lftp/4.8 | None | application | system | LFTP is a sophisticated file transfer program supporting a number of network protocols (ftp, http, sftp, fish, torrent). |
+| lynx | 2.8.8 | lynx/2.8 | None | application | tool | Lynx is a text browser for the World Wide Web. |
+| macs2 | 2.1.1 | macs2/2.1 | None | application | computational biology | MACS -- Model-based Analysis of ChIP-Seq |
+| maker | 2.31.9 | maker/2 | None | application | computational biology | MAKER is a genome annotation pipeline for prokaryotic and smaller eukaryotic organisms. |
+| mapsplice | 2.2.0 | mapsplice/2.2 | None | application | computational biology | MapSplice is a software for mapping RNA-seq data to reference genome for splice junction discovery that depends only on reference genome, and not on any further annotations. |
+| mathematica | 10.0 | mathematica/10.0 | None | application | unknown | |
+| mathematica | 10.4 | mathematica/10.4 | None | application | unknown | |
+| mathematica | 11.0 | mathematica/11.0 | None | application | unknown | |
+| mathematica | 9.0 | mathematica/9.0 | None | application | unknown | |
+| matlab | r2012b | matlab/r2012b | None | application | unknown | |
+| matlab | r2013b | matlab/r2013b | None | application | unknown | |
+| matlab | r2014b | matlab/r2014b | None | application | unknown | |
+| matlab | r2015b | matlab/r2015b | None | application | unknown | |
+| matlab | r2016a | matlab/r2016a | None | application | unknown | |
+| matlab | r2016b | matlab/r2016b | None | application | unknown | |
+| matlab | r2017a | matlab/r2017a | None | application | unknown | |
+| matlab | r2017b | matlab/r2017b | None | application | unknown | |
+| matlab | r2018a | matlab/r2018a | None | application | unknown | |
+| mbuffer | 20171011 | mbuffer/20171011 | None | application | buffer | Mbuffer is a tool for buffering data streams with a large set of unique features. |
+| mcl | 14.137 | mcl/14.137 | None | application | computational biology | MCL |
+| megahit | 1.1 | megahit/1.1 | None | application | computational biology | MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. |
+| metasv | 0.5.4 | metasv/0.5 | None | application | computational biology | An accurate and integrative structural-variant caller for next generation sequencing. |
+| mlpack | 3.0.3 | mlpack/3.0 | None | library | Machine Learning | mlpack a fast, flexible machine learning library |
+| multiqc | 1.6 | multiqc/py27/1.6 | None None None | application | computational biology | MultiQC is a tool to create a single report with interactive plots for multiple bioinformatics analyses across many samples. |
+| mummer4 | 4.0.0beta2 | mummer4/4.0 | None | application | Bioinformatics | MUMmer is a system for rapidly aligning entire genomes |
+| mxnet | 0.9.3a | mxnet/0.9.3 | None | application | AI | MXNet is an open-source deep learning framework that allows you to define, train, and deploy deep neural networks on a wide array of devices, from cloud infrastructure to mobile devices. |
+| ncbi-download | 0.2.6 | ncbi-download/0.2 | None | application | computational biology | Python scriopt for downloading bacterial and fungal genomes from NCBI. |
+| neper | 3.3.0 | neper/3.3 | None | application | Applications | Neper is a software package for polycrystal generation and meshing. |
+| octave | 4.2 | octave/4.2 | None | application | engineering | GNU Octave is a high-level language, primarily intended for numerical computations. It provides a convenient command line interface for solving linear and nonlinear problems numerically, and for performing other numerical experiments using a language that is mostly compatible with Matlab. |
+| opencv | 3.4.1 | opencv/py27/3.4 | None None | library | unknown | OpenCV is a computer vision and machine learning software library. |
+| orthofinder | 1.1.8 | orthofinder/1.1 | None | application | computational biology | OrthoFinder is a fast, accurate and comprehensive analysis tool for comparative genomics. |
+| orthofinder | 2.2.6 | orthofinder/2.2 | None | application | computational biology | OrthoFinder is a fast, accurate and comprehensive analysis tool for comparative genomics. |
+| paml | 4.9 | paml/4.9 | None | application | Sequencing | Phylogenetic Analysis by Maximum Likelihood (PAML) |
+| pandaseq | 2.11 | pandaseq/2.11 | None | application | bioinformatics | PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence. |
+| peakranger | 1.18 | peakranger/1.18 | None | application | computational biology | PeakRanger is a multi-purporse software suite for analyzing next-generation sequencing (NGS) data. |
+| peakzilla | 1.0 | peakzilla/1.0 | None | application | computational biology | Peakzilla identifies sites of enrichment and transcription factor binding sites from transcription factor ChIP-seq and ChIP-exo experiments at hight accuracy and resolution. |
+| pepr | 1.1.18 | pepr/1.1 | None | application | computational biology | Peak-calling and Prioritization pipeline for replicated ChIP-Seq data. |
+| perl | 5.22 | perl/5.22 | None | application | perl | The Perl Programming Language |
+| phylosnp | 1.0 | phylosnp/1.0 | None | application | computational biology | PhyloSNP is designed to take SNP data files (.csv and .vcf) and generate phylogenetic trees from the provided data. |
+| picard | 2.18.4 | picard/2.18 | None | application | computational biology | A set of Java command line tools for manipulating high-throughput sequencing data (HTS) data and formats. |
+| picard | 2.9.0 | picard/2.9 | None | application | computational biology | A set of Java command line tools for manipulating high-throughput sequencing data (HTS) data and formats. |
+| pindel | 0.2.5b9 | pindel/0.2 | None | application | computational biology | |
+| pirs | 2.0.2 | pirs/2.0 | None | application | computational biology | |
+| plink | 1.90b4 | plink/1.90 | None | application | computational biology | PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. |
+| plinkseq | 0.10 | plinkseq/0.10 | None | application | computational biology | PLINK/SEQ is an open-source C/C++ library for working with human genetic variation data. |
+| pomoxis | 0.1.7 | pomoxis/0.1 | None | application | computational biology | Pomoxis comprises APIs and command line tools for interacting and analysing Oxford Nanopore Technologies’ data in real time. |
+| prokka | 1.12 | prokka/1.12 | None | application | bioinformatics | Prokka is a software tool for the rapid annotation of prokaryotic genomes. |
+| pullseq | 1.0 | pullseq/1.0 | None | application | computational biology | pullseq - Software to extract sequence from a fasta or fastq. Also filter sequences by a minimum length or maximum length. |
+| pyclone | 0.13 | pyclone/0.13 | None | application | computational biology | PyClone is statistical model and software tool designed to infer the prevalence of point mutations in heterogeneous cancer samples. |
+| pyfasta | 0.5 | pyfasta/0.5 | None | application | computational biology | Pyfasta - fast, memory-efficient, pythonic (and command-line) access to fasta sequence files. |
+| pygenometracks | 2.0 | pygenometracks/2.0 | None | application | bioinformatics | Standalone program and library to plot beautiful genome browser tracks. |
+| pymongo | 3.0.3 | pymongo/3.0 | None | application | Utility | PyMongo is a Python distribution containing tools for working with MongoDB, and is the recommended way to work with MongoDB from Python. |
+| pymongo | 3.3.0 | pymongo/3.3 | None | application | Utility | PyMongo is a Python distribution containing tools for working with MongoDB, and is the recommended way to work with MongoDB from Python. |
+| python | 2.7 | python/2.7 | None | application | system | |
+| python | 3.4 | python/3.4 | None | application | system | |
+| python | 3.5 | python/3.5 | None | application | system | |
+| python | 3.6 | python/3.6 | None | application | system | |
+| python | 3.7 | python/3.7 | None | application | system | |
+| pytorch | 0.4.0 | pytorch/py36/0.4 | None None None | application | deep learning | PyTorch is an optimized tensor library for deep learning using GPUs and CPUs. |
+| qiime2 | 2018.4 | qiime2/2018.4 | None | application | computational biology | QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency. |
+| quasr | 6.09 | quasr/6.09 | None | application | computational biology | QUASR is lightweight pipeline for processing and analysis of high-throughput sequencing data. |
+| quast | 4.4 | quast/4.4 | None | application | computational biology | QUAST evaluates genome assemblies by computing various metrics. |
+| quast | 4.5 | quast/4.5 | None | application | computational biology | QUAST evaluates genome assemblies by computing various metrics. |
+| R | 3.4.4 | R/3.4 | None | application | mathematics | Microsoft R Open is the enhanced distribution of R from Microsoft Corporation. |
+| R | 3.5.1 | R/3.5 | None | application | mathematics | Microsoft R Open is the enhanced distribution of R from Microsoft Corporation. |
+| rarefactionanalyzer | 2018.09.06 | rarefactionanalyzer/2018.09.06 | None | application | computational biology | Rarefaction analyzer is a simple program that can be used to perform rarefaction analysis. |
+| rclone | 1.44 | rclone/1.44 | None | application | Storage | Rclone - rsync for cloud storage. |
+| red | 2015.05.22 | red/2015.05.22 | None | application | Genomics | Red (RepeatsDetector): an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale. |
+| regtools | 0.5.0 | regtools/0.5 | None | application | bioinformatics | Tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context. |
+| repenrich | 1.2 | repenrich/1.2 | None | application | computational biology | RepEnrich is a method to estimate repetitive element enrichment using high-throughput sequencing data. |
+| resistomeanalyzer | 2018.09.06 | resistomeanalyzer/2018.09.06 | None | application | computational biology | Resistome Analyzer is a simple tool for analyzing the resistome of large metagenomic datasets. |
+| revtrans | 1.4 | revtrans/1.4 | None | application | computational biology | RevTrans - performs a reverse translation of a peptide alignment. |
+| r-genometricorr | 1.1.17 | r-genometricorr/1.1 | None | application | Genomics | Genometric Correlation (GenometriCorr) is an R package for spatial correlation of genome-wide interval datasets. |
+| r-ggfortify | 0.4.1 | r-ggfortify/0.4 | None | application | r | ggfortify is a package of unified plotting tools for statistics commonly used, such as GLM, time series, PCA families, clustering and survival analysis. |
+| rgt | 0.11.4 | rgt/0.11 | None | application | computational biology | Toolkit to perform regulatory genomics data analysis |
+| r-markdown | 0.8 | r-markdown/0.8 | None | application | R | Markdown is a plain-text formatting syntax that can be converted to XHTML or other formats. |
+| rnastructure | 6.1 | rnastructure/6.1 | None | application | Bioinformatics | RNAstructure is a complete package for RNA and DNA secondary structure prediction and analysis. It includes algorithms for secondary structure prediction, including facility to predict base pairing probabilities. It also can be used to predict bimolecular structures and can predict the equilibrium binding affinity of an oligonucleotide to a structured RNA target. This is useful for siRNA design. It can also predict secondary structures common to two, unaligned sequences, which is much more accurate than single sequence secondary structure prediction. Finally, RNAstructure can take a number of different types of experiment mapping data to constrain or restrain structure prediction. These include chemical mapping, enzymatic mapping, NMR, and SHAPE data. |
+| r-regresshaplo | 1.0 | r-regresshaplo/1.0 | None | application | biology | This package reconstructs haplotypes from a BAM file using a penalized regression approach. |
+| r-scimpute | 0.0.6 | r-scimpute/0.0.6 | None | application | biology | scImpute is accurate and robust imputation of single-cell RNA sequencing data. |
+| rsem | 1.3 | rsem/1.3 | None | application | computational biology | RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. |
+| r-seqminer | 6.0 | r-seqminer/6.0 | None | application | biology | SEQMINER is for sequencing variant annotation, data integration and query in R. |
+| r-vcfr | 1.5.0 | r-vcfr/1.5 | None | application | biology | A package to manipulate and visualize VCF data in R. |
+| salmon | 0.6.0 | salmon/0.6 | None | application | computational biology | Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments. |
+| salmon | 0.8.2 | salmon/0.8 | None | application | computational biology | Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments. |
+| salmon | 0.9.1 | salmon/0.9 | None | application | computational biology | Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments. |
+| samtools | 1.5 | samtools/1.5 | None | application | computational biology | SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. |
+| samtools | 1.6 | samtools/1.6 | None | application | computational biology | SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. |
+| samtools | 1.9 | samtools/1.9 | None | application | computational biology | Tools for dealing with SAM, BAM and CRAM files |
+| sas | 9.3 | sas/9.3 | None | application | Applications | SAS is a software suite developed by SAS Institute for advanced analytics, business intelligence, data management, and predictive analytics. |
+| sas | 9.4 | sas/9.4 | None | application | Applications | SAS is a software suite developed by SAS Institute for advanced analytics, business intelligence, data management, and predictive analytics. |
+| scons | 2.5 | scons/2.5 | None | application | utility | SCons: A software construction tool. |
+| scons | 3.0 | scons/3.0 | None | application | utility | SCons: A software construction tool. |
+| seedme | 1.2 | seedme/1.2 | None | application | Utility | Client program for SeedMe.org. |
+| selecton | 2.4 | selecton/2.4 | None | application | Bioinformatics | Selecton 2007: advanced models for detecting positive and purifying selection using a Bayesian inference approach. |
+| seqtk | 1.2 | seqtk/1.2 | None | application | computational biology | Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. |
+| seqyclean | 1.10.07 | seqyclean/1.10 | None | application | Bioinformatics | Main purpose of this software is to pre-process NGS data in order to prepare for downstream analysis. |
+| shapeit | 2.0 | shapeit/2.0 | None | application | computational biology | SHAPEIT is a fast and accurate method for estimation of haplotypes (aka phasing) from genotype or sequencing data. |
+| sift4g | 2.0.0 | sift4g/2.0 | None | application | computational biology | SIFT 4G is a faster version of SIFT that enables us to scale up and provide SIFT predictions for more organisms. |
+| singularity | 2.2 | singularity/2.2 | None | application | system | Application containers enabling mobility of compute. |
+| singularity | 2.3 | singularity/2.3 | None | application | system | Application containers enabling mobility of compute. |
+| singularity | 2.4 | singularity/2.4 | None | application | system | Application containers enabling mobility of compute. |
+| singularity | 2.6 | singularity/2.6 | None | application | system | Application containers enabling mobility of compute. |
+| snpeff | 4.3 | snpeff/4.3 | None | application | computational biology | Genetic variant annotation and effect prediction toolbox. |
+| snpfinder | 1.0.0 | snpfinder/1.0 | None | application | computational biology | SNPFinder is a simple alignment-based haplotype variant caller that can be used with metagenomic sequence data. |
+| snp-pipeline | 0.7 | snp-pipeline/0.7 | None | application | computational biology | SNP Pipeline is a pipeline for the production of SNP matrices from sequence data used in the phylogenetic analysis of pathogenic organisms sequenced from samples of interest to food safety. |
+| snp-pipeline | 1.0 | snp-pipeline/1.0 | None | application | unknown | |
+| snp-sites | 2.3.3 | snp-sites/2.3 | None | application | computational biology | SNP-sites rapidly extracts SNPs from a multi-FASTA alignment. |
+| soapdenovo-trans | 1.04 | soapdenovo-trans/1.04 | None | application | computational biology | SOAPdenovo-Trans is a de novo transcriptome assembler basing on the SOAPdenovo framework, adapt to alternative splicing and different expression level among transcripts. |
+| sonnet | 1.13 | sonnet/py27/1.13 | None None None | application | machine learning | Sonnet is a library built on top of TensorFlow for building complex neural networks. |
+| sonnet | 1.19 | sonnet/py27/1.19 | None None None | application | machine learning | Sonnet is a library built on top of TensorFlow for building complex neural networks. |
+| sonnet | 1.23 | sonnet/py35/1.23 | None None None | application | machine learning | Sonnet is a library built on top of TensorFlow for building complex neural networks. |
+| spades | 3.10.1 | spades/3.10 | None | application | computational biology | SPAdes - St. Petersburg genome assembler - is intended for both standard isolates and single-cell MDA bacteria assemblies. |
+| spades | 3.11.1 | spades/3.11 | None | application | computational biology | SPAdes - St. Petersburg genome assembler - is intended for both standard isolates and single-cell MDA bacteria assemblies. |
+| spades | 3.12.0 | spades/3.12 | None | application | computational biology | SPAdes - St. Petersburg genome assembler - is intended for both standard isolates and single-cell MDA bacteria assemblies. |
+| spades | 3.8.1 | spades/3.8 | None | application | computational biology | SPAdes - St. Petersburg genome assembler - is intended for both standard isolates and single-cell MDA bacteria assemblies. |
+| ssake | 4.0 | ssake/4.0 | None | application | genomics | SSAKE is a genomics application for de novo assembly of millions of very short DNA sequences. |
+| stereogene | 2.20 | stereogene/2.20 | None | application | sequencing | StereoGene: Rapid Estimation of Genomewide Correlation of Continuous or Interval Feature Data |
+| targetfinder | 1.7 | targetfinder/1.7 | None | application | computational biology | Plant small RNA target prediction tool. |
+| tassel | 5.2.40 | tassel/5.2 | None | application | computational biology | TASSEL is a software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium. |
+| tax2tree | 1.0 | tax2tree/1.0 | None | application | computational biology | tax2tree - Tools for decorating taxonomy information on to a phylogenetic tree. |
+| tensorflow | 1.11.0 | tensorflow/py27/1.11 | None None | application | machine learning | TensorFlow is an open source software library for numerical computation using data flow graphs. |
+| theano | 0.9.0 | theano/py27/0.9 | None None None | application | mathematics | Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently. |
+| theano | 1.0.2 | theano/py36/1.0 | None None None | application | mathematics | Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently. |
+| transdecoder | 3.0.1 | transdecoder/3.0 | None | application | computational biology | TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. |
+| treemix | 1.13 | treemix/1.13 | None | application | computational biology | TreeMix is a method for inferring the patterns of population splits and mixtures in the history of a set of populations. |
+| trimmomatic | 0.36 | trimmomatic/0.36 | None | application | computational biology | Trimmomatic: A flexible read trimming tool for Illumina NGS data. |
+| trimmomatic | 0.38 | trimmomatic/0.38 | None | application | computational biology | A flexible read trimming tool for Illumina NGS data |
+| trinity | 2.4.0 | trinity/2.4 | None | application | computational biology | Trinity assembles transcript sequences from Illumina RNA-Seq data. |
+| trinity | 2.6.6 | trinity/2.6 | None | application | computational biology | Trinity RNA-Seq de novo transcriptome assembly |
+| ucsc-liftover | 366 | ucsc-liftover/366 | None | application | computational biology | The Batch Coordinate Conversion (liftOver) utility converts genome coordinates and genome annotation files between assemblies. |
+| viennarna | 2.3.3 | viennarna/2.3 | None | application | computational biology | The ViennaRNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures. |
+| xcrysden | 1.5.60 | xcrysden/1.5 | None | application | physics | XCrySDen is a crystalline and molecular structure visualisation program aiming at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated. |
+| zerone | 1.0 | zerone/1.0 | None | application | computational biology | Zerone discretizes several ChIP-seq replicates simultaneously and resolves conflicts between them. After the job is done, Zerone checks the results and tells you whether it passes the quality control. |
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+[hcc\_modules.xml](attachments/6946875/35326397.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/6946875/35326493.xml) (text/xml)
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+[hcc\_modules.xml](attachments/6946875/35326543.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/6946875/35326582.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/6946875/35326633.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/6946875/35326655.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/6946875/35326813.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/6946875/8126469.xml)
+(application/octet-stream)
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+[crane\_modules.xml](attachments/6946875/15171683.xml)
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+[crane\_modules.xml](attachments/6946875/15172537.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/6946875/35326890.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/6946875/35326925.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/6946875/35326944.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/6946875/35327026.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/6946875/35324468.xml) (text/xml)
+
+Document generated by Confluence on Oct 24, 2018 14:48
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/available_software_for_sandhills.md b/content/guides/running_applications/available_software_for_sandhills.md
new file mode 100644
index 00000000..f4cdabab
--- /dev/null
+++ b/content/guides/running_applications/available_software_for_sandhills.md
@@ -0,0 +1,5709 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Running Applications](Running-Applications_7471153.html)
+
+<span id="title-text"> HCC-DOCS : Available Software for Sandhills </span>
+==========================================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified by
+<span class="editor"> Natasha Pavlovikj</span> on Aug 07, 2018
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-approve confluence-information-macro-icon"></span>
+
+HCC provides some software packages via the Singularity container
+software. If you do not see a desired package in the module list below,
+please check the [Using
+Singularity](https://hcc-docs.unl.edu/display/HCCDOC/Using+Singularity) page
+for the software list there.
+
+Module prerequisites
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-warning confluence-information-macro-icon"></span>
+
+If a module lists one or more prerequisites, the prerequisite module(s)
+must be loaded before or along with, that module.
+
+For example, the `cdo/2.1` modules requires `compiler/pgi/13.` To load
+the cdo module, doing either
+
+`module load compiler/pgi/13module load cdo/2.1`
+
+or
+
+`module load compiler/pgi/13 cdo/2.1` (Note the prerequisite module
+**must** be first.)
+
+is acceptable.
+
+Multiple versions
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-info confluence-information-macro-icon"></span>
+
+Some packages list multiple compilers for prerequisites. This means that
+the package has been built with each version of the compilers listed.
+
+<table>
+<thead>
+<tr class="header">
+<th>Name</th>
+<th>Version</th>
+<th>Module Name</th>
+<th>Prerequisite(s)</th>
+<th>Type</th>
+<th>Domain</th>
+<th>Description</th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td>abinit</td>
+<td>8.0.8</td>
+<td>abinit/8.0</td>
+<td>compiler/intel/12:openmpi/1.8<br />
+</td>
+<td>application</td>
+<td>computational chemistry</td>
+<td>ABINIT is a package whose main program allows one to find the total energy.</td>
+</tr>
+<tr class="even">
+<td>acml</td>
+<td>5.3</td>
+<td>acml/5.3</td>
+<td>compiler/gcc/4.7<br />
+compiler/intel/11<br />
+compiler/intel/12<br />
+compiler/intel/13<br />
+compiler/pgi/11<br />
+compiler/pgi/12<br />
+compiler/pgi/13<br />
+compiler/pgi/14<br />
+compiler/pgi/15<br />
+</td>
+<td>library</td>
+<td>runtime support</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>anaconda</td>
+<td>2.7</td>
+<td>anaconda/2.7</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>system</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>anaconda</td>
+<td>3.3</td>
+<td>anaconda/3.3</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>system</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>anaconda</td>
+<td>3.4</td>
+<td>anaconda/3.4</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>system</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>anaconda</td>
+<td>4.3</td>
+<td>anaconda/4.3</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>system</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>ant</td>
+<td>4.6</td>
+<td>ant/1.8</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>Utility</td>
+<td>Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files as targets and extension points dependent upon each other.</td>
+</tr>
+<tr class="even">
+<td>atk</td>
+<td>13.8.2</td>
+<td>atk/13.8.2</td>
+<td>compiler/gcc/4.7:mpich2/1.5<br />
+</td>
+<td>application</td>
+<td>Chemistry</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>atk</td>
+<td>2014.1</td>
+<td>atk/2014.1</td>
+<td>compiler/gcc/4.7:mpich2/1.5<br />
+</td>
+<td>application</td>
+<td>Chemistry</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>atk</td>
+<td>2015.1</td>
+<td>atk/2015.1</td>
+<td>compiler/gcc/4.7:mpich2/1.5<br />
+</td>
+<td>application</td>
+<td>Chemistry</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>boost</td>
+<td>1.64</td>
+<td>boost/1.64</td>
+<td>compiler/gcc/7.1<br />
+</td>
+<td>application</td>
+<td>System Environment/Base</td>
+<td>Boost provides free peer-reviewed portable C++ source libraries.</td>
+</tr>
+<tr class="even">
+<td>boost</td>
+<td>1.66</td>
+<td>boost/1.66</td>
+<td>compiler/gcc/8.2<br />
+</td>
+<td>application</td>
+<td>System Environment/Base</td>
+<td>Boost provides free peer-reviewed portable C++ source libraries.</td>
+</tr>
+<tr class="odd">
+<td>cdo</td>
+<td>1.6</td>
+<td>cdo/1.6</td>
+<td>compiler/pgi/12<br />
+</td>
+<td>library</td>
+<td>runtime support</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>cdo</td>
+<td>1.7</td>
+<td>cdo/1.7</td>
+<td>compiler/pgi/12<br />
+</td>
+<td>library</td>
+<td>runtime support</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>clustal-omega</td>
+<td>1.2</td>
+<td>clustal-omega/1.2</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>Clustal Omega is the latest addition to the Clustal family. It offers a significant increase in scalability over previous versions, allowing hundreds of thousands of sequences to be aligned in only a few hours</td>
+</tr>
+<tr class="even">
+<td>compiler/gcc</td>
+<td>4.7</td>
+<td>compiler/gcc/4.7</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>compiler</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>compiler/gcc</td>
+<td>4.8</td>
+<td>compiler/gcc/4.8</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>compiler</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>compiler/gcc</td>
+<td>4.9</td>
+<td>compiler/gcc/4.9</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>compiler</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>compiler/gcc</td>
+<td>6.1</td>
+<td>compiler/gcc/6.1</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>compiler</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>compiler/gcc</td>
+<td>7.1</td>
+<td>compiler/gcc/7.1</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>compiler</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>compiler/gcc</td>
+<td>8.2</td>
+<td>compiler/gcc/8.2</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>compiler</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>compiler/intel</td>
+<td>11</td>
+<td>compiler/intel/11</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>compiler</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>compiler/intel</td>
+<td>12</td>
+<td>compiler/intel/12</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>compiler</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>compiler/intel</td>
+<td>13</td>
+<td>compiler/intel/13</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>compiler</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>compiler/intel</td>
+<td>15</td>
+<td>compiler/intel/15</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>compiler</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>compiler/intel</td>
+<td>16</td>
+<td>compiler/intel/16</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>compiler</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>compiler/intel</td>
+<td>18</td>
+<td>compiler/intel/18</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>compiler</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>compiler/open64</td>
+<td>4.5</td>
+<td>compiler/open64/4.5</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>compiler</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>compiler/pgi</td>
+<td>11</td>
+<td>compiler/pgi/11</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>compiler</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>compiler/pgi</td>
+<td>12</td>
+<td>compiler/pgi/12</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>compiler</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>compiler/pgi</td>
+<td>13</td>
+<td>compiler/pgi/13</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>compiler</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>compiler/pgi</td>
+<td>14</td>
+<td>compiler/pgi/14</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>compiler</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>compiler/pgi</td>
+<td>15</td>
+<td>compiler/pgi/15</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>compiler</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>compiler/pgi</td>
+<td>16</td>
+<td>compiler/pgi/16</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>compiler</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>cp2k</td>
+<td>2.6</td>
+<td>cp2k/2.6</td>
+<td>compiler/gcc/4.7:openmpi/1.6<br />
+</td>
+<td>library</td>
+<td>runtime support</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>cp2k</td>
+<td>3.0</td>
+<td>cp2k/3.0</td>
+<td>compiler/gcc/4.7:openmpi/1.8<br />
+</td>
+<td>library</td>
+<td>runtime support</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>cplex</td>
+<td>12.5</td>
+<td>cplex/12.5</td>
+<td>None<br />
+</td>
+<td>library</td>
+<td>runtime</td>
+<td>CPLEX - High-performance mathematical programming solver for linear programming, mixed integer programming, and quadratic programming.</td>
+</tr>
+<tr class="even">
+<td>dmtcp</td>
+<td>2.5</td>
+<td>dmtcp/2.5</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>Utility</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>elk</td>
+<td>4.3.6</td>
+<td>elk/4.3</td>
+<td>compiler/intel/13:openmpi/1.8<br />
+</td>
+<td>library</td>
+<td>runtime support</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>espresso</td>
+<td>5.0</td>
+<td>espresso/5.0</td>
+<td>compiler/intel/13:openmpi/1.6<br />
+</td>
+<td>library</td>
+<td>runtime support</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>espresso</td>
+<td>6.2.1</td>
+<td>espresso/6.2</td>
+<td>compiler/intel/15:openmpi/1.8<br />
+</td>
+<td>library</td>
+<td>runtime support</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>fftw3</td>
+<td>3.3</td>
+<td>fftw3/3.3</td>
+<td>compiler/intel/13<br />
+compiler/intel/15<br />
+</td>
+<td>library</td>
+<td>runtime support</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>gamess</td>
+<td>20141205R1</td>
+<td>gamess/20141205R1</td>
+<td>compiler/intel/13:openmpi/1.6<br />
+</td>
+<td>library</td>
+<td>runtime support</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>gdal</td>
+<td>2.2</td>
+<td>gdal/2.2</td>
+<td>compiler/gcc/4.7<br />
+</td>
+<td>library</td>
+<td>runtime support</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>gromacs</td>
+<td>4.6</td>
+<td>gromacs/4.6</td>
+<td>compiler/gcc/4.7:openmpi/1.6<br />
+</td>
+<td>library</td>
+<td>runtime support</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>GSL</td>
+<td>2.1</td>
+<td>GSL/2.1</td>
+<td>compiler/gcc/4.9<br />
+</td>
+<td>library</td>
+<td>runtime support</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>hdf4</td>
+<td>4.2</td>
+<td>hdf4/4.2</td>
+<td>compiler/gcc/4.7<br />
+compiler/intel/11<br />
+compiler/intel/12<br />
+compiler/pgi/12<br />
+</td>
+<td>library</td>
+<td>runtime support</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>hdf5</td>
+<td>1.8</td>
+<td>hdf5/1.8</td>
+<td>compiler/gcc/4.7<br />
+compiler/intel/11<br />
+compiler/intel/12<br />
+compiler/pgi/12<br />
+</td>
+<td>library</td>
+<td>runtime support</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>hdf5</td>
+<td>1.8.6</td>
+<td>hdf5/1.8.6</td>
+<td>compiler/intel/12<br />
+</td>
+<td>library</td>
+<td>runtime support</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>hdfeos2</td>
+<td>2.18</td>
+<td>hdfeos2/2.18</td>
+<td>compiler/gcc/4.7<br />
+compiler/intel/11<br />
+compiler/intel/12<br />
+compiler/pgi/12<br />
+</td>
+<td>library</td>
+<td>runtime support</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>hdfeos5</td>
+<td>1.14</td>
+<td>hdfeos5/1.14</td>
+<td>compiler/gcc/4.7<br />
+compiler/intel/11<br />
+compiler/intel/12<br />
+compiler/pgi/12<br />
+</td>
+<td>library</td>
+<td>runtime support</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>intel-mkl</td>
+<td>12</td>
+<td>intel-mkl/11</td>
+<td>None<br />
+None<br />
+</td>
+<td>library</td>
+<td>tools</td>
+<td>Numerical library, contains blas/lapack</td>
+</tr>
+<tr class="odd">
+<td>intel-mkl</td>
+<td>13</td>
+<td>intel-mkl/13</td>
+<td>None<br />
+</td>
+<td>library</td>
+<td>tools</td>
+<td>Numerical library, contains blas/lapack</td>
+</tr>
+<tr class="even">
+<td>intel-mkl</td>
+<td>15</td>
+<td>intel-mkl/15</td>
+<td>None<br />
+</td>
+<td>library</td>
+<td>tools</td>
+<td>Numerical library, contains blas/lapack</td>
+</tr>
+<tr class="odd">
+<td>intel-mkl</td>
+<td>16</td>
+<td>intel-mkl/16</td>
+<td>None<br />
+</td>
+<td>library</td>
+<td>tools</td>
+<td>Numerical library, contains blas/lapack</td>
+</tr>
+<tr class="even">
+<td>jasper</td>
+<td>1.900.1</td>
+<td>jasper/1.900</td>
+<td>compiler/gcc/4.7<br />
+</td>
+<td>library</td>
+<td>runtime support</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>jellyfish</td>
+<td>2.2.6</td>
+<td>jellyfish/2.2</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.</td>
+</tr>
+<tr class="even">
+<td>jellyfish</td>
+<td>2.2.7</td>
+<td>jellyfish/2.2</td>
+<td>compiler/gcc/4.9<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.</td>
+</tr>
+<tr class="odd">
+<td>lammps</td>
+<td>10Feb2017</td>
+<td>lammps/10Feb2017</td>
+<td>compiler/gcc/4.9:openmpi/1.8<br />
+</td>
+<td>library</td>
+<td>runtime support</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>lammps</td>
+<td>15MAY2015</td>
+<td>lammps/15May15</td>
+<td>compiler/gcc/4.9:openmpi/1.6<br />
+compiler/gcc/4.9:openmpi/1.8<br />
+</td>
+<td>library</td>
+<td>runtime support</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>lammps</td>
+<td>31MAR2017</td>
+<td>lammps/31Mar2017</td>
+<td>compiler/gcc/4.9:openmpi/1.8<br />
+</td>
+<td>library</td>
+<td>runtime support</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>libint</td>
+<td>1.1</td>
+<td>libint/1.1</td>
+<td>compiler/gcc/4.7<br />
+</td>
+<td>application</td>
+<td>Computational Chemistry</td>
+<td>Libint is a software stack for computing integrals used in molecular quantum mechanics</td>
+</tr>
+<tr class="odd">
+<td>libxc</td>
+<td>2.2.3</td>
+<td>libxc/2.2</td>
+<td>compiler/intel/13<br />
+</td>
+<td>library</td>
+<td>runtime support</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>lsdyna</td>
+<td>8.0.0</td>
+<td>lsdyna/8.0.0</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>unknown</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>lsdyna</td>
+<td>8.0.1</td>
+<td>lsdyna/8.0.1</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>unknown</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>lsdyna</td>
+<td>8.1.0</td>
+<td>lsdyna/8.1.0</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>unknown</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>lsdyna</td>
+<td>9.0.1</td>
+<td>lsdyna/9.0.1</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>unknown</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>maven</td>
+<td>3.5</td>
+<td>maven/3.5</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>system</td>
+<td>Apache Maven is a software project management and comprehension tool.</td>
+</tr>
+<tr class="odd">
+<td>mpich2</td>
+<td>1.5</td>
+<td>mpich2/1.5</td>
+<td>compiler/gcc/4.7<br />
+</td>
+<td>library</td>
+<td>runtime support</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>multiwell</td>
+<td>2017</td>
+<td>multiwell/2017</td>
+<td>compiler/gcc/4.9:openmpi/1.8<br />
+</td>
+<td>application</td>
+<td>chemistry</td>
+<td>MultiWell calculates time dependent concentrations, reaction yields, vibrational distributions, and rate constants as functions of temperature and pressure for multi-well, multi-channel unimolecular reactions systems that consist of stable species and multiple isomerization and/or dissociation reactions.</td>
+</tr>
+<tr class="odd">
+<td>NCL</td>
+<td>6.0</td>
+<td>NCL/6.0dist</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>utility</td>
+<td>A library of graphics utilites from the Natl. Center for Atmospheric Research.</td>
+</tr>
+<tr class="even">
+<td>NCL</td>
+<td>6.1</td>
+<td>NCL/6.1dist</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>utility</td>
+<td>A library of graphics utilites from the Natl. Center for Atmospheric Research.</td>
+</tr>
+<tr class="odd">
+<td>NCL</td>
+<td>6.3</td>
+<td>NCL/6.3dist</td>
+<td>None<br />
+None<br />
+</td>
+<td>application</td>
+<td>utility</td>
+<td>A library of graphics utilites from the Natl. Center for Atmospheric Research.</td>
+</tr>
+<tr class="even">
+<td>NCL</td>
+<td>6.4</td>
+<td>NCL/6.4</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>utility</td>
+<td>A library of graphics utilites from the Natl. Center for Atmospheric Research.</td>
+</tr>
+<tr class="odd">
+<td>NCO</td>
+<td>4.2</td>
+<td>NCO/4.2</td>
+<td>compiler/gcc/4.7<br />
+compiler/intel/11<br />
+compiler/intel/12<br />
+compiler/pgi/12<br />
+</td>
+<td>library</td>
+<td>runtime support</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>netcdf</td>
+<td>4.1</td>
+<td>netcdf/4.1</td>
+<td>compiler/pgi/12<br />
+</td>
+<td>library</td>
+<td>runtime support</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>netcdf</td>
+<td>4.2</td>
+<td>netcdf/4.2</td>
+<td>compiler/gcc/4.7<br />
+compiler/intel/11<br />
+compiler/intel/12<br />
+compiler/pgi/12<br />
+</td>
+<td>library</td>
+<td>runtime support</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>nwchem</td>
+<td>6.5</td>
+<td>nwchem/6.5</td>
+<td>compiler/intel/13:openmpi/1.6<br />
+</td>
+<td>library</td>
+<td>runtime support</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>nwchem</td>
+<td>6.6</td>
+<td>nwchem/6.6</td>
+<td>compiler/intel/13:openmpi/1.8<br />
+</td>
+<td>library</td>
+<td>runtime support</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>openmpi</td>
+<td>1.10.4</td>
+<td>openmpi/1.10</td>
+<td>compiler/intel/15<br />
+compiler/intel/16<br />
+</td>
+<td>library</td>
+<td>runtime support</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>openmpi</td>
+<td>1.6</td>
+<td>openmpi/1.6</td>
+<td>compiler/gcc/4.7<br />
+compiler/gcc/4.8<br />
+compiler/gcc/4.9<br />
+compiler/intel/11<br />
+compiler/intel/12<br />
+compiler/intel/13<br />
+compiler/open64/4.5<br />
+compiler/pgi/11<br />
+compiler/pgi/12<br />
+compiler/pgi/13<br />
+compiler/pgi/14<br />
+compiler/pgi/15<br />
+</td>
+<td>library</td>
+<td>runtime support</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>openmpi</td>
+<td>1.8</td>
+<td>openmpi/1.8</td>
+<td>compiler/gcc/4.7<br />
+compiler/gcc/4.8<br />
+compiler/gcc/4.9<br />
+compiler/intel/11<br />
+compiler/intel/12<br />
+compiler/intel/13<br />
+compiler/intel/15<br />
+compiler/pgi/11<br />
+compiler/pgi/12<br />
+compiler/pgi/13<br />
+</td>
+<td>library</td>
+<td>runtime support</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>openmx</td>
+<td>3.7</td>
+<td>openmx/3.7</td>
+<td>compiler/intel/13:openmpi/1.6<br />
+</td>
+<td>library</td>
+<td>runtime support</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>openmx</td>
+<td>3.8</td>
+<td>openmx/3.8</td>
+<td>compiler/intel/13:openmpi/1.8<br />
+</td>
+<td>library</td>
+<td>runtime support</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>proj</td>
+<td>4.9</td>
+<td>proj/4.9</td>
+<td>compiler/gcc/4.7<br />
+</td>
+<td>library</td>
+<td>runtime support</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>python</td>
+<td>3.3</td>
+<td>python/3.3</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>system</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>python-openstackclient</td>
+<td>3.3</td>
+<td>python-openstackclient/3.3</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>Utility</td>
+<td>OpenStackClient (aka OSC) is a command-line client for OpenStack that brings the command set for Compute, Identity, Image, Object Store and Block Storage APIs together in a single shell with a uniform command structure.</td>
+</tr>
+<tr class="even">
+<td>R</td>
+<td>2.15</td>
+<td>R/2.15</td>
+<td>None<br />
+</td>
+<td>library</td>
+<td>runtime support</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>R</td>
+<td>3.0</td>
+<td>R/3.0</td>
+<td>None<br />
+</td>
+<td>library</td>
+<td>runtime support</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>R</td>
+<td>3.2</td>
+<td>R/3.2</td>
+<td>None<br />
+</td>
+<td>library</td>
+<td>runtime support</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>ruby</td>
+<td>2.0</td>
+<td>ruby/2.0</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>system</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>scientificpython</td>
+<td>2.8.1</td>
+<td>scientificpython/2.8</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>scientific computing</td>
+<td>ScientificPython is a collection of Python modules that are useful for scientific computing.</td>
+</tr>
+<tr class="odd">
+<td>shtns</td>
+<td>2.6</td>
+<td>shtns/2.6</td>
+<td>compiler/intel/15<br />
+</td>
+<td>application</td>
+<td>math</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>siesta</td>
+<td>4.1.3</td>
+<td>siesta/4.1</td>
+<td>compiler/gcc/4.9:openmpi/1.8<br />
+compiler/intel/13:openmpi/1.8<br />
+</td>
+<td>library</td>
+<td>runtime support</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>SRAtoolkit</td>
+<td>2.8.2</td>
+<td>SRAtoolkit/2.8</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>SRA Toolkit</td>
+</tr>
+<tr class="even">
+<td>szip</td>
+<td>2.1</td>
+<td>szip/2.1</td>
+<td>compiler/gcc/4.7<br />
+compiler/intel/11<br />
+compiler/intel/12<br />
+compiler/pgi/12<br />
+</td>
+<td>library</td>
+<td>runtime support</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>tensorflow</td>
+<td>0.12.1</td>
+<td>tensorflow/py35/0.12</td>
+<td>None<br />
+None<br />
+</td>
+<td>application</td>
+<td>machine learning</td>
+<td>TensorFlow is an open source software library for numerical computation using data flow graphs.</td>
+</tr>
+<tr class="even">
+<td>tensorflow</td>
+<td>1.0.0</td>
+<td>tensorflow/py35/1.0</td>
+<td>None<br />
+None<br />
+</td>
+<td>application</td>
+<td>machine learning</td>
+<td>TensorFlow is an open source software library for numerical computation using data flow graphs.</td>
+</tr>
+<tr class="odd">
+<td>tensorflow</td>
+<td>1.3.1</td>
+<td>tensorflow/py35/1.3</td>
+<td>None<br />
+None<br />
+None<br />
+</td>
+<td>application</td>
+<td>machine learning</td>
+<td>TensorFlow is an open source software library for numerical computation using data flow graphs.</td>
+</tr>
+<tr class="even">
+<td>tensorflow</td>
+<td>1.4.0</td>
+<td>tensorflow/py36/1.4</td>
+<td>None<br />
+None<br />
+None<br />
+</td>
+<td>application</td>
+<td>machine learning</td>
+<td>TensorFlow is an open source software library for numerical computation using data flow graphs.</td>
+</tr>
+<tr class="odd">
+<td>tensorflow</td>
+<td>1.5.0</td>
+<td>tensorflow/py35/1.5</td>
+<td>None<br />
+None<br />
+None<br />
+</td>
+<td>application</td>
+<td>machine learning</td>
+<td>TensorFlow is an open source software library for numerical computation using data flow graphs.</td>
+</tr>
+<tr class="even">
+<td>udunits</td>
+<td>2.1</td>
+<td>udunits/2.1</td>
+<td>compiler/pgi/12<br />
+</td>
+<td>library</td>
+<td>runtime support</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>vasp</td>
+<td>5.4</td>
+<td>vasp/5.4sol</td>
+<td>compiler/intel/13:openmpi/1.6<br />
+compiler/intel/13:openmpi/1.6<br />
+</td>
+<td>library</td>
+<td>runtime support</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>vasp</td>
+<td>5.4.4</td>
+<td>vasp/5.4.4</td>
+<td>compiler/intel/15:openmpi/1.8<br />
+</td>
+<td>library</td>
+<td>runtime support</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>viennarna</td>
+<td>2.4.5</td>
+<td>viennarna/2.4</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>The ViennaRNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.</td>
+</tr>
+<tr class="even">
+<td>WRF</td>
+<td>WRF</td>
+<td>WRF/WRF</td>
+<td>None<br />
+</td>
+<td>library</td>
+<td>runtime support</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>zlib</td>
+<td>1.2</td>
+<td>zlib/1.2</td>
+<td>compiler/gcc/4.7<br />
+compiler/intel/11<br />
+compiler/intel/12<br />
+compiler/open64/4.5<br />
+compiler/pgi/12<br />
+</td>
+<td>library</td>
+<td>runtime support</td>
+<td></td>
+</tr>
+</tbody>
+</table>
+
+<table>
+<thead>
+<tr class="header">
+<th>Name</th>
+<th>Version</th>
+<th>Module Name</th>
+<th>Prerequisite(s)</th>
+<th>Type</th>
+<th>Domain</th>
+<th>Description</th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td>abayesqr</td>
+<td>1.0</td>
+<td>abayesqr/1.0</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>high-throughput sequencing data</td>
+<td>aBayesQR is a viral quasispecies reconstruction algorithm that employs a maximum-likelihood framework to infer individual sequences in a mixture from high-throughput sequencing data.</td>
+</tr>
+<tr class="even">
+<td>afni</td>
+<td>18.2.06</td>
+<td>afni/18.2</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>MRI</td>
+<td>AFNI is a suite of programs for looking at and analyzing 3D brain images.</td>
+</tr>
+<tr class="odd">
+<td>afterqc</td>
+<td>0.9.6</td>
+<td>afterqc/0.9</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>package</td>
+<td>Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data. AfterQC can simply go through all fastq files in a folder and then output three folders: good, bad and QC folders, which contains good reads, bad reads and the QC results of each fastq file/pair. Currently it supports processing data from HiSeq 2000/2500/3000/4000, Nextseq 500/550, MiniSeq...and other Illumina 1.8 or newer formats.</td>
+</tr>
+<tr class="even">
+<td>agfusion</td>
+<td>1.0</td>
+<td>agfusion/1.0</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>Biology</td>
+<td>AGFusion is a python package for annotating gene fusions from the human or mouse genomes.</td>
+</tr>
+<tr class="odd">
+<td>allinea</td>
+<td>18.0</td>
+<td>allinea/18.0</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>Utility</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>allinea</td>
+<td>18.2</td>
+<td>allinea/18.2</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>Utility</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>allinea</td>
+<td>4.2</td>
+<td>allinea/4.2</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>Utility</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>allinea</td>
+<td>5.0</td>
+<td>allinea/5.0</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>Utility</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>allinea</td>
+<td>5.1</td>
+<td>allinea/5.1</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>Utility</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>allinea</td>
+<td>6.0</td>
+<td>allinea/6.0</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>Utility</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>allinea</td>
+<td>6.1</td>
+<td>allinea/6.1</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>Utility</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>allinea</td>
+<td>7.0</td>
+<td>allinea/7.0</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>Utility</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>ant</td>
+<td>1.10.1</td>
+<td>ant/1.10</td>
+<td>None<br />
+</td>
+<td>library</td>
+<td>java</td>
+<td>Java build tool</td>
+</tr>
+<tr class="even">
+<td>ant</td>
+<td>1.9.9</td>
+<td>ant/1.9</td>
+<td>None<br />
+</td>
+<td>library</td>
+<td>java</td>
+<td>Java build tool</td>
+</tr>
+<tr class="odd">
+<td>apkid</td>
+<td>1.0.0</td>
+<td>apkid/1.0</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>Malware</td>
+<td>APKiD is Android Application Identifier for Packers, Protectors, Obfuscators and Oddities - PEiD for Android.</td>
+</tr>
+<tr class="even">
+<td>aria2</td>
+<td>1.23.0</td>
+<td>aria2/1.23</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>tool</td>
+<td>aria2 is a lightweight multi-protocol & multi-source command-line download utility.</td>
+</tr>
+<tr class="odd">
+<td>aspera-cli</td>
+<td>3.7.7</td>
+<td>aspera-cli/3.7</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>system</td>
+<td>IBM Aspera Command-Line Interface (the Aspera CLI) is a collection of Aspera tools for performing high-speed, secure data transfers from the command line.</td>
+</tr>
+<tr class="even">
+<td>augustus</td>
+<td>3.2.3</td>
+<td>augustus/3.2</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke and Oliver Keller. It can be used as an ab initio program, which means it bases its prediction purely on the sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources such as EST, MS/MS, protein alignments and synthenic genomic alignments.</td>
+</tr>
+<tr class="odd">
+<td>augustus</td>
+<td>3.3</td>
+<td>augustus/3.3</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke and Oliver Keller. It can be used as an ab initio program, which means it bases its prediction purely on the sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources such as EST, MS/MS, protein alignments and synthenic genomic alignments.</td>
+</tr>
+<tr class="even">
+<td>autoconf</td>
+<td>2.69</td>
+<td>autoconf/2.69</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>Utilities</td>
+<td>Extensible M4 macros that produce shell scripts to configure software source code packages.</td>
+</tr>
+<tr class="odd">
+<td>autodock</td>
+<td>4.2.6</td>
+<td>autodock/4.2</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>Chemistry</td>
+<td>AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.</td>
+</tr>
+<tr class="even">
+<td>awscli</td>
+<td>1.1.120</td>
+<td>awscli/1.11</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>utility</td>
+<td>The AWS CLI is an open source tool built on top of the AWS SDK for Python (Boto) that provides commands for interacting with AWS services.</td>
+</tr>
+<tr class="odd">
+<td>bam-readcount</td>
+<td>0.8</td>
+<td>bam-readcount/0.8</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>The purpose of this program is to generate metrics at single nucleotide positions.</td>
+</tr>
+<tr class="even">
+<td>bamtools</td>
+<td>2.3.0</td>
+<td>bamtools/2.3</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>C++ API & command-line toolkit for working with BAM data</td>
+</tr>
+<tr class="odd">
+<td>bamtools</td>
+<td>2.4.1</td>
+<td>bamtools/2.4</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>C++ API & command-line toolkit for working with BAM data</td>
+</tr>
+<tr class="even">
+<td>bbmap</td>
+<td>37.17</td>
+<td>bbmap/37.17</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>BBMap is a splice-aware global aligner for DNA and RNA sequencing reads.</td>
+</tr>
+<tr class="odd">
+<td>bbmap</td>
+<td>38.06</td>
+<td>bbmap/38.06</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>BBMap is a splice-aware global aligner for DNA and RNA sequencing reads.</td>
+</tr>
+<tr class="even">
+<td>bcftools</td>
+<td>1.3.1</td>
+<td>bcftools/1.3</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.</td>
+</tr>
+<tr class="odd">
+<td>bcftools</td>
+<td>1.8</td>
+<td>bcftools/1.8</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.</td>
+</tr>
+<tr class="even">
+<td>beagle</td>
+<td>4.1_21Jan17</td>
+<td>beagle/4.1</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>Biology</td>
+<td>Beagle is a software package that performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection.</td>
+</tr>
+<tr class="odd">
+<td>beast</td>
+<td>1.8</td>
+<td>beast/1.8</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>biology</td>
+<td>BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC.</td>
+</tr>
+<tr class="even">
+<td>beast2</td>
+<td>2.4</td>
+<td>beast2/2.4</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>biology</td>
+<td>BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences.</td>
+</tr>
+<tr class="odd">
+<td>bedops</td>
+<td>2.4.35</td>
+<td>bedops/2.4</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale.</td>
+</tr>
+<tr class="even">
+<td>bedtools</td>
+<td>2.24.0</td>
+<td>bedtools/2.24</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>A powerful toolset for genome arithmetic</td>
+</tr>
+<tr class="odd">
+<td>bedtools</td>
+<td>2.27.1</td>
+<td>bedtools/2.27</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>A powerful toolset for genome arithmetic</td>
+</tr>
+<tr class="even">
+<td>beta</td>
+<td>1.0.7</td>
+<td>beta/1.0</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>Binding and Expression Target Analysis (BETA) is a software package that integrates ChIP-seq of transcription factors or chromatin regulators with differential gene expression data to infer direct target genes.</td>
+</tr>
+<tr class="odd">
+<td>binutils</td>
+<td>2.30</td>
+<td>binutils/2.30</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>Utilities</td>
+<td>The GNU Binutils are a collection of binary tools.</td>
+</tr>
+<tr class="even">
+<td>bioconductor</td>
+<td>3.4</td>
+<td>bioconductor/3.4</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data.</td>
+</tr>
+<tr class="odd">
+<td>bioconductor-ballgown</td>
+<td>2.2.0</td>
+<td>bioconductor-ballgown/2.2</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>Tools for statistical analysis of assembled transcriptomes, including flexible differential expression analysis, visualization of transcript structures, and matching of assembled transcripts to annotation.</td>
+</tr>
+<tr class="even">
+<td>bioconductor-jmosaics</td>
+<td>1.10</td>
+<td>bioconductor-jmosaics/1.10</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>Joint analysis of multiple ChIP-Seq data sets.</td>
+</tr>
+<tr class="odd">
+<td>biodata</td>
+<td>1.0</td>
+<td>biodata/1.0</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>Static data resources for bioinformatics/computational biology.</td>
+</tr>
+<tr class="even">
+<td>biom-format</td>
+<td>2.1</td>
+<td>biom-format/2.1</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>The BIOM file format (canonically pronounced biome) is designed to be a general-use format for representing biological sample by observation contingency tables. BIOM is a recognized standard for the Earth Microbiome Project and is a Genomics Standards Consortium supported project.</td>
+</tr>
+<tr class="odd">
+<td>bioperl</td>
+<td>1.6.924</td>
+<td>bioperl/1.6.924</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>BioPerl - Perl Modules for Biology</td>
+</tr>
+<tr class="even">
+<td>biopython</td>
+<td>1.70</td>
+<td>biopython/py36/1.70</td>
+<td>None<br />
+None<br />
+None<br />
+</td>
+<td>library</td>
+<td>biological computation</td>
+<td>Biopython is a set of freely available tools for biological computation written in Python by an international team of developers.</td>
+</tr>
+<tr class="odd">
+<td>biopython</td>
+<td>1.71</td>
+<td>biopython/py27/1.71</td>
+<td>None<br />
+None<br />
+None<br />
+</td>
+<td>library</td>
+<td>biological computation</td>
+<td>Biopython is a set of freely available tools for biological computation written in Python by an international team of developers.</td>
+</tr>
+<tr class="even">
+<td>blast</td>
+<td>2.6.0</td>
+<td>blast/2.6</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>NCBI BLAST+ sequence alignment package. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches.</td>
+</tr>
+<tr class="odd">
+<td>blast</td>
+<td>2.7.1</td>
+<td>blast/2.7</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>NCBI BLAST+ sequence alignment package. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches.</td>
+</tr>
+<tr class="even">
+<td>breakdancer</td>
+<td>1.4</td>
+<td>breakdancer/1.4</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>BreakDancer is a Perl/C++ package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads.</td>
+</tr>
+<tr class="odd">
+<td>breakseq2</td>
+<td>2.2</td>
+<td>breakseq2/2.2</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>BreakSeq2: Ultrafast and accurate nucleotide-resolution analysis of structural variants.</td>
+</tr>
+<tr class="even">
+<td>bsmap</td>
+<td>2.90</td>
+<td>bsmap/2.90</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>Mapping</td>
+<td>BSMAP is a short reads mapping software for bisulfite sequencing reads.</td>
+</tr>
+<tr class="odd">
+<td>bx-python</td>
+<td>0.8.1</td>
+<td>bx-python/py27/0.8</td>
+<td>None<br />
+None<br />
+None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>Tools for manipulating biological data, particularly multiple sequence alignments</td>
+</tr>
+<tr class="even">
+<td>canu</td>
+<td>1.7</td>
+<td>canu/1.7</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>Canu is a fork of the Celera Assembler, designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION).</td>
+</tr>
+<tr class="odd">
+<td>ccat</td>
+<td>3.0</td>
+<td>ccat/3.0</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>A software package for the analysis of ChIP-seq data with negative control.</td>
+</tr>
+<tr class="even">
+<td>clove</td>
+<td>0.17</td>
+<td>clove/0.17</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>CLOVE: Classification of genomic fusions into structural variation events.</td>
+</tr>
+<tr class="odd">
+<td>clustalw</td>
+<td>2.1</td>
+<td>clustalw/2.1</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>ClustalW2 is a multiple sequence alignment tool for the alignment of DNA or protein sequences.</td>
+</tr>
+<tr class="even">
+<td>cmake</td>
+<td>2.8.10.2</td>
+<td>cmake/2.8</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>system</td>
+<td>CMake is an extensible, open-source system that manages the build process</td>
+</tr>
+<tr class="odd">
+<td>cmake</td>
+<td>3.10.3</td>
+<td>cmake/3.10</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>system</td>
+<td>CMake is an extensible, open-source system that manages the build process</td>
+</tr>
+<tr class="even">
+<td>cmake</td>
+<td>3.11.3</td>
+<td>cmake/3.11</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>system</td>
+<td>CMake is an extensible, open-source system that manages the build process</td>
+</tr>
+<tr class="odd">
+<td>cmake</td>
+<td>3.5.0</td>
+<td>cmake/3.5</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>system</td>
+<td>CMake is an extensible, open-source system that manages the build process</td>
+</tr>
+<tr class="even">
+<td>cmake</td>
+<td>3.7.1</td>
+<td>cmake/3.7</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>system</td>
+<td>CMake is an extensible, open-source system that manages the build process</td>
+</tr>
+<tr class="odd">
+<td>codonw</td>
+<td>1.4.4</td>
+<td>codonw/1.4</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>CodonW is a programme designed to simplify the Multivariate analysis (correspondence analysis) of codon and amino acid usage.</td>
+</tr>
+<tr class="even">
+<td>connectome-workbench</td>
+<td>1.3.1</td>
+<td>connectome-workbench/1.3</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>neuroimaging</td>
+<td>Connectome Workbench is an open source, freely available visualization and discovery tool used to map neuroimaging data, especially data generated by the Human Connectome Project</td>
+</tr>
+<tr class="odd">
+<td>cutadapt</td>
+<td>1.13</td>
+<td>cutadapt/1.13</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>NGS data</td>
+<td>Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.</td>
+</tr>
+<tr class="even">
+<td>cutadapt</td>
+<td>1.4</td>
+<td>cutadapt/1.4</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>Cutadapt removes adapter sequences from DNA high-throughput sequencing data.</td>
+</tr>
+<tr class="odd">
+<td>deap</td>
+<td>1.0</td>
+<td>deap/1.0</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computer science</td>
+<td>DEAP is a novel evolutionary computation framework for rapid prototyping and testing of ideas.</td>
+</tr>
+<tr class="even">
+<td>deeptools</td>
+<td>2.5.4</td>
+<td>deeptools/2.5</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>detectron/py27</td>
+<td>2018.09.11</td>
+<td>detectron/py27/2018.09.11</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>object detection</td>
+<td>FAIR's research platform for object detection research, implementing popular algorithms like Mask R-CNN and RetinaNet.</td>
+</tr>
+<tr class="even">
+<td>eigen</td>
+<td>3.3.3</td>
+<td>eigen/3.3</td>
+<td>None<br />
+</td>
+<td>library</td>
+<td>C++</td>
+<td>C++ template library for linear algebra</td>
+</tr>
+<tr class="odd">
+<td>entrez-direct</td>
+<td>10.0</td>
+<td>entrez-direct/10.0</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>Entrez</td>
+<td>Entrez Direct (EDirect) is an advanced method for accessing the NCBI's set of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window. Functions take search terms from command-line arguments. Individual operations are combined to build multi-step queries. Record retrieval and formatting normally complete the process.</td>
+</tr>
+<tr class="even">
+<td>eqtlbma</td>
+<td>1.3</td>
+<td>eqtlbma/1.3</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>biology</td>
+<td>Package to detect eQTLs jointly in multiple subgroups (e.g. tissues) via Bayesian Model Averaging.</td>
+</tr>
+<tr class="odd">
+<td>fastqc</td>
+<td>0.11.7</td>
+<td>fastqc/0.11</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>fastqc - A Quality Control application for FastQ files</td>
+</tr>
+<tr class="even">
+<td>fasttree</td>
+<td>2.1.10</td>
+<td>fasttree/2.1</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.</td>
+</tr>
+<tr class="odd">
+<td>fqtrim</td>
+<td>0.9.7</td>
+<td>fqtrim/0.9</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>fqtrim: trimming & filtering of NGS reads.</td>
+</tr>
+<tr class="even">
+<td>freebayes</td>
+<td>1.2.0</td>
+<td>freebayes/1.2</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>Biology</td>
+<td>Bayesian haplotype-based polymorphism discovery and genotyping</td>
+</tr>
+<tr class="odd">
+<td>freesurfer</td>
+<td>5.3.0</td>
+<td>freesurfer/5.3</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational neuroimaging</td>
+<td>An open source software suite for processing and analyzing (human) brain MRI images.</td>
+</tr>
+<tr class="even">
+<td>freesurfer</td>
+<td>6.0.0</td>
+<td>freesurfer/6.0</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational neuroimaging</td>
+<td>An open source software suite for processing and analyzing (human) brain MRI images.</td>
+</tr>
+<tr class="odd">
+<td>gatk4</td>
+<td>4.0.4.0</td>
+<td>gatk4/4.0</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>GATK4: This toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping.</td>
+</tr>
+<tr class="even">
+<td>gaussian</td>
+<td>09 RevD</td>
+<td>gaussian/09/RevD</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>Chemistry</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>gaussian</td>
+<td>09 RevE</td>
+<td>gaussian/09/RevE</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>Chemistry</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>gaussian</td>
+<td>16 RevE</td>
+<td>gaussian/16/RevA</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>Chemistry</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>gdcclient</td>
+<td>1.3.0</td>
+<td>gdcclient/1.3</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>genomics</td>
+<td>GDC provides a standard client-based mechanism in support of high performance data downloads and submission.</td>
+</tr>
+<tr class="even">
+<td>gem</td>
+<td>2.7</td>
+<td>gem/2.7</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>GEM: High resolution peak calling and motif discovery for ChIP-seq and ChIP-exo data.</td>
+</tr>
+<tr class="odd">
+<td>geoparse</td>
+<td>1.0.5</td>
+<td>geoparse/1.0</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>Bioinformatics</td>
+<td>Python library to access Gene Expression Omnibus Database (GEO)</td>
+</tr>
+<tr class="even">
+<td>ghostscript</td>
+<td>9.20</td>
+<td>ghostscript/9.20</td>
+<td>None<br />
+</td>
+<td>library</td>
+<td>runtime support</td>
+<td>An interpreter for the PostScript language and for PDF.</td>
+</tr>
+<tr class="odd">
+<td>ghostscript</td>
+<td>9.22</td>
+<td>ghostscript/9.22</td>
+<td>None<br />
+</td>
+<td>library</td>
+<td>runtime support</td>
+<td>An interpreter for the PostScript language and for PDF.</td>
+</tr>
+<tr class="even">
+<td>git</td>
+<td>2.17.0</td>
+<td>git/2.17</td>
+<td>None<br />
+</td>
+<td>library</td>
+<td>tools</td>
+<td>distributed version control system</td>
+</tr>
+<tr class="odd">
+<td>git</td>
+<td>2.7.4</td>
+<td>git/2.7</td>
+<td>None<br />
+</td>
+<td>library</td>
+<td>tools</td>
+<td>distributed version control system</td>
+</tr>
+<tr class="even">
+<td>globus-cli</td>
+<td>1.2.0</td>
+<td>globus-cli/1.2</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>tool</td>
+<td>Command line clients provide an interface to Globus services from the shell, and are suited for both interactive use and simple scripting use cases.</td>
+</tr>
+<tr class="odd">
+<td>glpk</td>
+<td>4.61</td>
+<td>glpk/4.61</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>mathematics</td>
+<td>The GLPK (GNU Linear Programming Kit) package is intended for solving large-scale linear programming (LP), mixed integer programming (MIP), and other related problems. It is a set of routines written in ANSI C and organized in the form of a callable library.</td>
+</tr>
+<tr class="even">
+<td>gmap</td>
+<td>2015.12.31</td>
+<td>gmap/2015.12.31</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and GSNAP: Genomic Short-read Nucleotide Alignment Program.</td>
+</tr>
+<tr class="odd">
+<td>gmap</td>
+<td>2017.05.08</td>
+<td>gmap/2017.05.08</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and GSNAP: Genomic Short-read Nucleotide Alignment Program.</td>
+</tr>
+<tr class="even">
+<td>gmap</td>
+<td>2018.03.25</td>
+<td>gmap/2018.03.25</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and GSNAP: Genomic Short-read Nucleotide Alignment Program.</td>
+</tr>
+<tr class="odd">
+<td>gnu-parallel</td>
+<td>20180522</td>
+<td>gnu-parallel/20180522</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>Shell tool</td>
+<td>GNU parallel is a shell tool for executing jobs in parallel using one or more computers.</td>
+</tr>
+<tr class="even">
+<td>gnuplot</td>
+<td>4.6.0</td>
+<td>gnuplot/4.6</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>unknown</td>
+<td>Gnuplot, plotting from command line</td>
+</tr>
+<tr class="odd">
+<td>gnuplot</td>
+<td>5.2.3</td>
+<td>gnuplot/5.2</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>unknown</td>
+<td>Gnuplot, plotting from command line</td>
+</tr>
+<tr class="even">
+<td>graphlan</td>
+<td>1.0.0</td>
+<td>graphlan/1.0</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>unknown</td>
+<td>GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. It focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation.</td>
+</tr>
+<tr class="odd">
+<td>graphviz</td>
+<td>2.38.0</td>
+<td>graphviz/2.38</td>
+<td>None<br />
+</td>
+<td>library</td>
+<td>unknown</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>gtdbtk</td>
+<td>0.1.3</td>
+<td>gtdbtk/0.1</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.</td>
+</tr>
+<tr class="odd">
+<td>hotspot3d</td>
+<td>0.6.0</td>
+<td>hotspot3d/0.6</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>bioinformatics</td>
+<td>This 3D proximity tool can be used to identify mutation hotspots from linear protein sequence and correlate the hotspots with known or potentially interacting domains, mutations, or drugs. Mutation-mutation and mutation-drug clusters can also be identified and viewed.</td>
+</tr>
+<tr class="even">
+<td>htseq</td>
+<td>0.5.4p5</td>
+<td>htseq/0.5.4p5</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>HTSeq - Analysing high-throughput sequencing data with Python</td>
+</tr>
+<tr class="odd">
+<td>htseq</td>
+<td>0.6.1p1</td>
+<td>htseq/0.6.1p1</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>HTSeq - Analysing high-throughput sequencing data with Python</td>
+</tr>
+<tr class="even">
+<td>htseq</td>
+<td>0.9.1</td>
+<td>htseq/0.9</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>HTSeq - Analysing high-throughput sequencing data with Python</td>
+</tr>
+<tr class="odd">
+<td>htslib</td>
+<td>1.7</td>
+<td>htslib/1.7</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>HTSlib is an implementation of a unified C library for accessing common file formats.</td>
+</tr>
+<tr class="even">
+<td>htstream</td>
+<td>e919d21</td>
+<td>htstream/e919d21</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>Bioinformatics</td>
+<td>A toolset for high throughput sequence analysis using a streaming approach facilitated by Linux pipes.</td>
+</tr>
+<tr class="odd">
+<td>imagemagick</td>
+<td>7.0.8_10</td>
+<td>imagemagick/7.0</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>bitmap</td>
+<td>Software suite to create, edit, compose, or convert bitmap images.</td>
+</tr>
+<tr class="even">
+<td>impute2</td>
+<td>2.3.2</td>
+<td>impute2/2.3</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>IMPUTE2 is a computer program for phasing observed genotypes and imputing missing genotypes.</td>
+</tr>
+<tr class="odd">
+<td>iqtree</td>
+<td>1.6.7</td>
+<td>iqtree/1.6</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>IQ-TREE creates phylogenetic trees under maximum likelihood with emphasis on speed and accuracy.</td>
+</tr>
+<tr class="even">
+<td>jamm</td>
+<td>1.0.7r2</td>
+<td>jamm/1.0.7r2</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>JAMM is a peak finder for NGS datasets (ChIP-Seq, ATAC-Seq, DNase-Seq..etc.) that can integrate replicates and assign peak boundaries accurately.</td>
+</tr>
+<tr class="odd">
+<td>java</td>
+<td>1.6</td>
+<td>java/1.6</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>system</td>
+<td>Java JDK.</td>
+</tr>
+<tr class="even">
+<td>java</td>
+<td>1.7</td>
+<td>java/1.7</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>system</td>
+<td>Java JDK.</td>
+</tr>
+<tr class="odd">
+<td>java</td>
+<td>1.8</td>
+<td>java/1.8</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>system</td>
+<td>Java JDK.</td>
+</tr>
+<tr class="even">
+<td>julia</td>
+<td>1.0</td>
+<td>julia/1.0</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>Language</td>
+<td>A high-performance dynamic programming language for data science</td>
+</tr>
+<tr class="odd">
+<td>jvarkit-msa2vcf</td>
+<td>1.0</td>
+<td>jvarkit-msa2vcf/1.0</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>Getting a VCF file from a CLUSTAW or a FASTA alignment.</td>
+</tr>
+<tr class="even">
+<td>jvarkit-sam2tsv</td>
+<td>1.0</td>
+<td>jvarkit-sam2tsv/1.0</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>Prints the SAM alignments as a TAB delimited file.</td>
+</tr>
+<tr class="odd">
+<td>kalign</td>
+<td>2.0</td>
+<td>kalign/2.0</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>Kalign is a fast and accurate multiple sequence alignment algorithm designed to align large numbers of protein sequences.</td>
+</tr>
+<tr class="even">
+<td>ksnp</td>
+<td>3.1</td>
+<td>ksnp/3.1</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>kSNP identifies the pan-genome SNPs in a set of genome sequences, and estimates phylogenetic trees based upon those SNPs.</td>
+</tr>
+<tr class="odd">
+<td>lftp</td>
+<td>4.8.3</td>
+<td>lftp/4.8</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>system</td>
+<td>LFTP is a sophisticated file transfer program supporting a number of network protocols (ftp, http, sftp, fish, torrent).</td>
+</tr>
+<tr class="even">
+<td>lynx</td>
+<td>2.8.8</td>
+<td>lynx/2.8</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>tool</td>
+<td>Lynx is a text browser for the World Wide Web.</td>
+</tr>
+<tr class="odd">
+<td>macs2</td>
+<td>2.1.1</td>
+<td>macs2/2.1</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>MACS -- Model-based Analysis of ChIP-Seq</td>
+</tr>
+<tr class="even">
+<td>maker</td>
+<td>2.31.9</td>
+<td>maker/2</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>MAKER is a genome annotation pipeline for prokaryotic and smaller eukaryotic organisms.</td>
+</tr>
+<tr class="odd">
+<td>mapsplice</td>
+<td>2.2.0</td>
+<td>mapsplice/2.2</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>MapSplice is a software for mapping RNA-seq data to reference genome for splice junction discovery that depends only on reference genome, and not on any further annotations.</td>
+</tr>
+<tr class="even">
+<td>mathematica</td>
+<td>10.0</td>
+<td>mathematica/10.0</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>unknown</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>mathematica</td>
+<td>10.4</td>
+<td>mathematica/10.4</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>unknown</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>mathematica</td>
+<td>11.0</td>
+<td>mathematica/11.0</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>unknown</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>mathematica</td>
+<td>9.0</td>
+<td>mathematica/9.0</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>unknown</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>matlab</td>
+<td>r2012b</td>
+<td>matlab/r2012b</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>unknown</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>matlab</td>
+<td>r2013b</td>
+<td>matlab/r2013b</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>unknown</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>matlab</td>
+<td>r2014b</td>
+<td>matlab/r2014b</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>unknown</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>matlab</td>
+<td>r2015b</td>
+<td>matlab/r2015b</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>unknown</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>matlab</td>
+<td>r2016a</td>
+<td>matlab/r2016a</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>unknown</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>matlab</td>
+<td>r2016b</td>
+<td>matlab/r2016b</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>unknown</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>matlab</td>
+<td>r2017a</td>
+<td>matlab/r2017a</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>unknown</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>matlab</td>
+<td>r2017b</td>
+<td>matlab/r2017b</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>unknown</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>matlab</td>
+<td>r2018a</td>
+<td>matlab/r2018a</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>unknown</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>mbuffer</td>
+<td>20171011</td>
+<td>mbuffer/20171011</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>buffer</td>
+<td>Mbuffer is a tool for buffering data streams with a large set of unique features.</td>
+</tr>
+<tr class="even">
+<td>mcl</td>
+<td>14.137</td>
+<td>mcl/14.137</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>MCL</td>
+</tr>
+<tr class="odd">
+<td>megahit</td>
+<td>1.1</td>
+<td>megahit/1.1</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.</td>
+</tr>
+<tr class="even">
+<td>metasv</td>
+<td>0.5.4</td>
+<td>metasv/0.5</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>An accurate and integrative structural-variant caller for next generation sequencing.</td>
+</tr>
+<tr class="odd">
+<td>mlpack</td>
+<td>3.0.3</td>
+<td>mlpack/3.0</td>
+<td>None<br />
+</td>
+<td>library</td>
+<td>Machine Learning</td>
+<td>mlpack a fast, flexible machine learning library</td>
+</tr>
+<tr class="even">
+<td>multiqc</td>
+<td>1.6</td>
+<td>multiqc/py27/1.6</td>
+<td>None<br />
+None<br />
+None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>MultiQC is a tool to create a single report with interactive plots for multiple bioinformatics analyses across many samples.</td>
+</tr>
+<tr class="odd">
+<td>mummer4</td>
+<td>4.0.0beta2</td>
+<td>mummer4/4.0</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>Bioinformatics</td>
+<td>MUMmer is a system for rapidly aligning entire genomes</td>
+</tr>
+<tr class="even">
+<td>mxnet</td>
+<td>0.9.3a</td>
+<td>mxnet/0.9.3</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>AI</td>
+<td>MXNet is an open-source deep learning framework that allows you to define, train, and deploy deep neural networks on a wide array of devices, from cloud infrastructure to mobile devices.</td>
+</tr>
+<tr class="odd">
+<td>ncbi-download</td>
+<td>0.2.6</td>
+<td>ncbi-download/0.2</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>Python scriopt for downloading bacterial and fungal genomes from NCBI.</td>
+</tr>
+<tr class="even">
+<td>neper</td>
+<td>3.3.0</td>
+<td>neper/3.3</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>Applications</td>
+<td>Neper is a software package for polycrystal generation and meshing.</td>
+</tr>
+<tr class="odd">
+<td>octave</td>
+<td>4.2</td>
+<td>octave/4.2</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>engineering</td>
+<td>GNU Octave is a high-level language, primarily intended for numerical computations. It provides a convenient command line interface for solving linear and nonlinear problems numerically, and for performing other numerical experiments using a language that is mostly compatible with Matlab.</td>
+</tr>
+<tr class="even">
+<td>opencv</td>
+<td>3.4.1</td>
+<td>opencv/py27/3.4</td>
+<td>None<br />
+None<br />
+</td>
+<td>library</td>
+<td>unknown</td>
+<td>OpenCV is a computer vision and machine learning software library.</td>
+</tr>
+<tr class="odd">
+<td>orthofinder</td>
+<td>1.1.8</td>
+<td>orthofinder/1.1</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>OrthoFinder is a fast, accurate and comprehensive analysis tool for comparative genomics.</td>
+</tr>
+<tr class="even">
+<td>orthofinder</td>
+<td>2.2.6</td>
+<td>orthofinder/2.2</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>OrthoFinder is a fast, accurate and comprehensive analysis tool for comparative genomics.</td>
+</tr>
+<tr class="odd">
+<td>paml</td>
+<td>4.9</td>
+<td>paml/4.9</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>Sequencing</td>
+<td>Phylogenetic Analysis by Maximum Likelihood (PAML)</td>
+</tr>
+<tr class="even">
+<td>pandaseq</td>
+<td>2.11</td>
+<td>pandaseq/2.11</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>bioinformatics</td>
+<td>PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.</td>
+</tr>
+<tr class="odd">
+<td>peakranger</td>
+<td>1.18</td>
+<td>peakranger/1.18</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>PeakRanger is a multi-purporse software suite for analyzing next-generation sequencing (NGS) data.</td>
+</tr>
+<tr class="even">
+<td>peakzilla</td>
+<td>1.0</td>
+<td>peakzilla/1.0</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>Peakzilla identifies sites of enrichment and transcription factor binding sites from transcription factor ChIP-seq and ChIP-exo experiments at hight accuracy and resolution.</td>
+</tr>
+<tr class="odd">
+<td>pepr</td>
+<td>1.1.18</td>
+<td>pepr/1.1</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>Peak-calling and Prioritization pipeline for replicated ChIP-Seq data.</td>
+</tr>
+<tr class="even">
+<td>perl</td>
+<td>5.22</td>
+<td>perl/5.22</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>perl</td>
+<td>The Perl Programming Language</td>
+</tr>
+<tr class="odd">
+<td>phylosnp</td>
+<td>1.0</td>
+<td>phylosnp/1.0</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>PhyloSNP is designed to take SNP data files (.csv and .vcf) and generate phylogenetic trees from the provided data.</td>
+</tr>
+<tr class="even">
+<td>picard</td>
+<td>2.18.4</td>
+<td>picard/2.18</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>A set of Java command line tools for manipulating high-throughput sequencing data (HTS) data and formats.</td>
+</tr>
+<tr class="odd">
+<td>picard</td>
+<td>2.9.0</td>
+<td>picard/2.9</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>A set of Java command line tools for manipulating high-throughput sequencing data (HTS) data and formats.</td>
+</tr>
+<tr class="even">
+<td>pindel</td>
+<td>0.2.5b9</td>
+<td>pindel/0.2</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>pirs</td>
+<td>2.0.2</td>
+<td>pirs/2.0</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>plink</td>
+<td>1.90b4</td>
+<td>plink/1.90</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.</td>
+</tr>
+<tr class="odd">
+<td>plinkseq</td>
+<td>0.10</td>
+<td>plinkseq/0.10</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>PLINK/SEQ is an open-source C/C++ library for working with human genetic variation data.</td>
+</tr>
+<tr class="even">
+<td>pomoxis</td>
+<td>0.1.7</td>
+<td>pomoxis/0.1</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>Pomoxis comprises APIs and command line tools for interacting and analysing Oxford Nanopore Technologies’ data in real time.</td>
+</tr>
+<tr class="odd">
+<td>prokka</td>
+<td>1.12</td>
+<td>prokka/1.12</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>bioinformatics</td>
+<td>Prokka is a software tool for the rapid annotation of prokaryotic genomes.</td>
+</tr>
+<tr class="even">
+<td>pullseq</td>
+<td>1.0</td>
+<td>pullseq/1.0</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>pullseq - Software to extract sequence from a fasta or fastq. Also filter sequences by a minimum length or maximum length.</td>
+</tr>
+<tr class="odd">
+<td>pyclone</td>
+<td>0.13</td>
+<td>pyclone/0.13</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>PyClone is statistical model and software tool designed to infer the prevalence of point mutations in heterogeneous cancer samples.</td>
+</tr>
+<tr class="even">
+<td>pyfasta</td>
+<td>0.5</td>
+<td>pyfasta/0.5</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>Pyfasta - fast, memory-efficient, pythonic (and command-line) access to fasta sequence files.</td>
+</tr>
+<tr class="odd">
+<td>pygenometracks</td>
+<td>2.0</td>
+<td>pygenometracks/2.0</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>bioinformatics</td>
+<td>Standalone program and library to plot beautiful genome browser tracks.</td>
+</tr>
+<tr class="even">
+<td>pymongo</td>
+<td>3.0.3</td>
+<td>pymongo/3.0</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>Utility</td>
+<td>PyMongo is a Python distribution containing tools for working with MongoDB, and is the recommended way to work with MongoDB from Python.</td>
+</tr>
+<tr class="odd">
+<td>pymongo</td>
+<td>3.3.0</td>
+<td>pymongo/3.3</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>Utility</td>
+<td>PyMongo is a Python distribution containing tools for working with MongoDB, and is the recommended way to work with MongoDB from Python.</td>
+</tr>
+<tr class="even">
+<td>python</td>
+<td>2.7</td>
+<td>python/2.7</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>system</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>python</td>
+<td>3.4</td>
+<td>python/3.4</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>system</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>python</td>
+<td>3.5</td>
+<td>python/3.5</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>system</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>python</td>
+<td>3.6</td>
+<td>python/3.6</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>system</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>python</td>
+<td>3.7</td>
+<td>python/3.7</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>system</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>pytorch</td>
+<td>0.4.0</td>
+<td>pytorch/py36/0.4</td>
+<td>None<br />
+None<br />
+None<br />
+</td>
+<td>application</td>
+<td>deep learning</td>
+<td>PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.</td>
+</tr>
+<tr class="even">
+<td>qiime2</td>
+<td>2018.4</td>
+<td>qiime2/2018.4</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency.</td>
+</tr>
+<tr class="odd">
+<td>quasr</td>
+<td>6.09</td>
+<td>quasr/6.09</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>QUASR is lightweight pipeline for processing and analysis of high-throughput sequencing data.</td>
+</tr>
+<tr class="even">
+<td>quast</td>
+<td>4.4</td>
+<td>quast/4.4</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>QUAST evaluates genome assemblies by computing various metrics.</td>
+</tr>
+<tr class="odd">
+<td>quast</td>
+<td>4.5</td>
+<td>quast/4.5</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>QUAST evaluates genome assemblies by computing various metrics.</td>
+</tr>
+<tr class="even">
+<td>R</td>
+<td>3.4.4</td>
+<td>R/3.4</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>mathematics</td>
+<td>Microsoft R Open is the enhanced distribution of R from Microsoft Corporation.</td>
+</tr>
+<tr class="odd">
+<td>R</td>
+<td>3.5.1</td>
+<td>R/3.5</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>mathematics</td>
+<td>Microsoft R Open is the enhanced distribution of R from Microsoft Corporation.</td>
+</tr>
+<tr class="even">
+<td>rarefactionanalyzer</td>
+<td>2018.09.06</td>
+<td>rarefactionanalyzer/2018.09.06</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>Rarefaction analyzer is a simple program that can be used to perform rarefaction analysis.</td>
+</tr>
+<tr class="odd">
+<td>rclone</td>
+<td>1.44</td>
+<td>rclone/1.44</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>Storage</td>
+<td>Rclone - rsync for cloud storage.</td>
+</tr>
+<tr class="even">
+<td>red</td>
+<td>2015.05.22</td>
+<td>red/2015.05.22</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>Genomics</td>
+<td>Red (RepeatsDetector): an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale.</td>
+</tr>
+<tr class="odd">
+<td>regtools</td>
+<td>0.5.0</td>
+<td>regtools/0.5</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>bioinformatics</td>
+<td>Tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context.</td>
+</tr>
+<tr class="even">
+<td>repenrich</td>
+<td>1.2</td>
+<td>repenrich/1.2</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>RepEnrich is a method to estimate repetitive element enrichment using high-throughput sequencing data.</td>
+</tr>
+<tr class="odd">
+<td>resistomeanalyzer</td>
+<td>2018.09.06</td>
+<td>resistomeanalyzer/2018.09.06</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>Resistome Analyzer is a simple tool for analyzing the resistome of large metagenomic datasets.</td>
+</tr>
+<tr class="even">
+<td>revtrans</td>
+<td>1.4</td>
+<td>revtrans/1.4</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>RevTrans - performs a reverse translation of a peptide alignment.</td>
+</tr>
+<tr class="odd">
+<td>r-genometricorr</td>
+<td>1.1.17</td>
+<td>r-genometricorr/1.1</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>Genomics</td>
+<td>Genometric Correlation (GenometriCorr) is an R package for spatial correlation of genome-wide interval datasets.</td>
+</tr>
+<tr class="even">
+<td>r-ggfortify</td>
+<td>0.4.1</td>
+<td>r-ggfortify/0.4</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>r</td>
+<td>ggfortify is a package of unified plotting tools for statistics commonly used, such as GLM, time series, PCA families, clustering and survival analysis.</td>
+</tr>
+<tr class="odd">
+<td>rgt</td>
+<td>0.11.4</td>
+<td>rgt/0.11</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>Toolkit to perform regulatory genomics data analysis</td>
+</tr>
+<tr class="even">
+<td>r-markdown</td>
+<td>0.8</td>
+<td>r-markdown/0.8</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>R</td>
+<td>Markdown is a plain-text formatting syntax that can be converted to XHTML or other formats.</td>
+</tr>
+<tr class="odd">
+<td>rnastructure</td>
+<td>6.1</td>
+<td>rnastructure/6.1</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>Bioinformatics</td>
+<td>RNAstructure is a complete package for RNA and DNA secondary structure prediction and analysis. It includes algorithms for secondary structure prediction, including facility to predict base pairing probabilities. It also can be used to predict bimolecular structures and can predict the equilibrium binding affinity of an oligonucleotide to a structured RNA target. This is useful for siRNA design. It can also predict secondary structures common to two, unaligned sequences, which is much more accurate than single sequence secondary structure prediction. Finally, RNAstructure can take a number of different types of experiment mapping data to constrain or restrain structure prediction. These include chemical mapping, enzymatic mapping, NMR, and SHAPE data.</td>
+</tr>
+<tr class="even">
+<td>r-regresshaplo</td>
+<td>1.0</td>
+<td>r-regresshaplo/1.0</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>biology</td>
+<td>This package reconstructs haplotypes from a BAM file using a penalized regression approach.</td>
+</tr>
+<tr class="odd">
+<td>r-scimpute</td>
+<td>0.0.6</td>
+<td>r-scimpute/0.0.6</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>biology</td>
+<td>scImpute is accurate and robust imputation of single-cell RNA sequencing data.</td>
+</tr>
+<tr class="even">
+<td>rsem</td>
+<td>1.3</td>
+<td>rsem/1.3</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data.</td>
+</tr>
+<tr class="odd">
+<td>r-seqminer</td>
+<td>6.0</td>
+<td>r-seqminer/6.0</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>biology</td>
+<td>SEQMINER is for sequencing variant annotation, data integration and query in R.</td>
+</tr>
+<tr class="even">
+<td>r-vcfr</td>
+<td>1.5.0</td>
+<td>r-vcfr/1.5</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>biology</td>
+<td>A package to manipulate and visualize VCF data in R.</td>
+</tr>
+<tr class="odd">
+<td>salmon</td>
+<td>0.6.0</td>
+<td>salmon/0.6</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments.</td>
+</tr>
+<tr class="even">
+<td>salmon</td>
+<td>0.8.2</td>
+<td>salmon/0.8</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments.</td>
+</tr>
+<tr class="odd">
+<td>salmon</td>
+<td>0.9.1</td>
+<td>salmon/0.9</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments.</td>
+</tr>
+<tr class="even">
+<td>samtools</td>
+<td>1.5</td>
+<td>samtools/1.5</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.</td>
+</tr>
+<tr class="odd">
+<td>samtools</td>
+<td>1.6</td>
+<td>samtools/1.6</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.</td>
+</tr>
+<tr class="even">
+<td>samtools</td>
+<td>1.9</td>
+<td>samtools/1.9</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>Tools for dealing with SAM, BAM and CRAM files</td>
+</tr>
+<tr class="odd">
+<td>sas</td>
+<td>9.3</td>
+<td>sas/9.3</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>Applications</td>
+<td>SAS is a software suite developed by SAS Institute for advanced analytics, business intelligence, data management, and predictive analytics.</td>
+</tr>
+<tr class="even">
+<td>sas</td>
+<td>9.4</td>
+<td>sas/9.4</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>Applications</td>
+<td>SAS is a software suite developed by SAS Institute for advanced analytics, business intelligence, data management, and predictive analytics.</td>
+</tr>
+<tr class="odd">
+<td>scons</td>
+<td>2.5</td>
+<td>scons/2.5</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>utility</td>
+<td>SCons: A software construction tool.</td>
+</tr>
+<tr class="even">
+<td>scons</td>
+<td>3.0</td>
+<td>scons/3.0</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>utility</td>
+<td>SCons: A software construction tool.</td>
+</tr>
+<tr class="odd">
+<td>seedme</td>
+<td>1.2</td>
+<td>seedme/1.2</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>Utility</td>
+<td>Client program for SeedMe.org.</td>
+</tr>
+<tr class="even">
+<td>selecton</td>
+<td>2.4</td>
+<td>selecton/2.4</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>Bioinformatics</td>
+<td>Selecton 2007: advanced models for detecting positive and purifying selection using a Bayesian inference approach.</td>
+</tr>
+<tr class="odd">
+<td>seqtk</td>
+<td>1.2</td>
+<td>seqtk/1.2</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format.</td>
+</tr>
+<tr class="even">
+<td>seqyclean</td>
+<td>1.10.07</td>
+<td>seqyclean/1.10</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>Bioinformatics</td>
+<td>Main purpose of this software is to pre-process NGS data in order to prepare for downstream analysis.</td>
+</tr>
+<tr class="odd">
+<td>shapeit</td>
+<td>2.0</td>
+<td>shapeit/2.0</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>SHAPEIT is a fast and accurate method for estimation of haplotypes (aka phasing) from genotype or sequencing data.</td>
+</tr>
+<tr class="even">
+<td>sift4g</td>
+<td>2.0.0</td>
+<td>sift4g/2.0</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>SIFT 4G is a faster version of SIFT that enables us to scale up and provide SIFT predictions for more organisms.</td>
+</tr>
+<tr class="odd">
+<td>singularity</td>
+<td>2.2</td>
+<td>singularity/2.2</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>system</td>
+<td>Application containers enabling mobility of compute.</td>
+</tr>
+<tr class="even">
+<td>singularity</td>
+<td>2.3</td>
+<td>singularity/2.3</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>system</td>
+<td>Application containers enabling mobility of compute.</td>
+</tr>
+<tr class="odd">
+<td>singularity</td>
+<td>2.4</td>
+<td>singularity/2.4</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>system</td>
+<td>Application containers enabling mobility of compute.</td>
+</tr>
+<tr class="even">
+<td>singularity</td>
+<td>2.6</td>
+<td>singularity/2.6</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>system</td>
+<td>Application containers enabling mobility of compute.</td>
+</tr>
+<tr class="odd">
+<td>snpeff</td>
+<td>4.3</td>
+<td>snpeff/4.3</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>Genetic variant annotation and effect prediction toolbox.</td>
+</tr>
+<tr class="even">
+<td>snpfinder</td>
+<td>1.0.0</td>
+<td>snpfinder/1.0</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>SNPFinder is a simple alignment-based haplotype variant caller that can be used with metagenomic sequence data.</td>
+</tr>
+<tr class="odd">
+<td>snp-pipeline</td>
+<td>0.7</td>
+<td>snp-pipeline/0.7</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>SNP Pipeline is a pipeline for the production of SNP matrices from sequence data used in the phylogenetic analysis of pathogenic organisms sequenced from samples of interest to food safety.</td>
+</tr>
+<tr class="even">
+<td>snp-pipeline</td>
+<td>1.0</td>
+<td>snp-pipeline/1.0</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>unknown</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>snp-sites</td>
+<td>2.3.3</td>
+<td>snp-sites/2.3</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>SNP-sites rapidly extracts SNPs from a multi-FASTA alignment.</td>
+</tr>
+<tr class="even">
+<td>soapdenovo-trans</td>
+<td>1.04</td>
+<td>soapdenovo-trans/1.04</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>SOAPdenovo-Trans is a de novo transcriptome assembler basing on the SOAPdenovo framework, adapt to alternative splicing and different expression level among transcripts.</td>
+</tr>
+<tr class="odd">
+<td>sonnet</td>
+<td>1.13</td>
+<td>sonnet/py27/1.13</td>
+<td>None<br />
+None<br />
+None<br />
+</td>
+<td>application</td>
+<td>machine learning</td>
+<td>Sonnet is a library built on top of TensorFlow for building complex neural networks.</td>
+</tr>
+<tr class="even">
+<td>sonnet</td>
+<td>1.19</td>
+<td>sonnet/py27/1.19</td>
+<td>None<br />
+None<br />
+None<br />
+</td>
+<td>application</td>
+<td>machine learning</td>
+<td>Sonnet is a library built on top of TensorFlow for building complex neural networks.</td>
+</tr>
+<tr class="odd">
+<td>sonnet</td>
+<td>1.23</td>
+<td>sonnet/py35/1.23</td>
+<td>None<br />
+None<br />
+None<br />
+</td>
+<td>application</td>
+<td>machine learning</td>
+<td>Sonnet is a library built on top of TensorFlow for building complex neural networks.</td>
+</tr>
+<tr class="even">
+<td>spades</td>
+<td>3.10.1</td>
+<td>spades/3.10</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>SPAdes - St. Petersburg genome assembler - is intended for both standard isolates and single-cell MDA bacteria assemblies.</td>
+</tr>
+<tr class="odd">
+<td>spades</td>
+<td>3.11.1</td>
+<td>spades/3.11</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>SPAdes - St. Petersburg genome assembler - is intended for both standard isolates and single-cell MDA bacteria assemblies.</td>
+</tr>
+<tr class="even">
+<td>spades</td>
+<td>3.12.0</td>
+<td>spades/3.12</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>SPAdes - St. Petersburg genome assembler - is intended for both standard isolates and single-cell MDA bacteria assemblies.</td>
+</tr>
+<tr class="odd">
+<td>spades</td>
+<td>3.8.1</td>
+<td>spades/3.8</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>SPAdes - St. Petersburg genome assembler - is intended for both standard isolates and single-cell MDA bacteria assemblies.</td>
+</tr>
+<tr class="even">
+<td>ssake</td>
+<td>4.0</td>
+<td>ssake/4.0</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>genomics</td>
+<td>SSAKE is a genomics application for de novo assembly of millions of very short DNA sequences.</td>
+</tr>
+<tr class="odd">
+<td>stereogene</td>
+<td>2.20</td>
+<td>stereogene/2.20</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>sequencing</td>
+<td>StereoGene: Rapid Estimation of Genomewide Correlation of Continuous or Interval Feature Data</td>
+</tr>
+<tr class="even">
+<td>targetfinder</td>
+<td>1.7</td>
+<td>targetfinder/1.7</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>Plant small RNA target prediction tool.</td>
+</tr>
+<tr class="odd">
+<td>tassel</td>
+<td>5.2.40</td>
+<td>tassel/5.2</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>TASSEL is a software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium.</td>
+</tr>
+<tr class="even">
+<td>tax2tree</td>
+<td>1.0</td>
+<td>tax2tree/1.0</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>tax2tree - Tools for decorating taxonomy information on to a phylogenetic tree.</td>
+</tr>
+<tr class="odd">
+<td>tensorflow</td>
+<td>1.11.0</td>
+<td>tensorflow/py27/1.11</td>
+<td>None<br />
+None<br />
+</td>
+<td>application</td>
+<td>machine learning</td>
+<td>TensorFlow is an open source software library for numerical computation using data flow graphs.</td>
+</tr>
+<tr class="even">
+<td>theano</td>
+<td>0.9.0</td>
+<td>theano/py27/0.9</td>
+<td>None<br />
+None<br />
+None<br />
+</td>
+<td>application</td>
+<td>mathematics</td>
+<td>Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently.</td>
+</tr>
+<tr class="odd">
+<td>theano</td>
+<td>1.0.2</td>
+<td>theano/py36/1.0</td>
+<td>None<br />
+None<br />
+None<br />
+</td>
+<td>application</td>
+<td>mathematics</td>
+<td>Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently.</td>
+</tr>
+<tr class="even">
+<td>transdecoder</td>
+<td>3.0.1</td>
+<td>transdecoder/3.0</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.</td>
+</tr>
+<tr class="odd">
+<td>treemix</td>
+<td>1.13</td>
+<td>treemix/1.13</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>TreeMix is a method for inferring the patterns of population splits and mixtures in the history of a set of populations.</td>
+</tr>
+<tr class="even">
+<td>trimmomatic</td>
+<td>0.36</td>
+<td>trimmomatic/0.36</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>Trimmomatic: A flexible read trimming tool for Illumina NGS data.</td>
+</tr>
+<tr class="odd">
+<td>trimmomatic</td>
+<td>0.38</td>
+<td>trimmomatic/0.38</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>A flexible read trimming tool for Illumina NGS data</td>
+</tr>
+<tr class="even">
+<td>trinity</td>
+<td>2.4.0</td>
+<td>trinity/2.4</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>Trinity assembles transcript sequences from Illumina RNA-Seq data.</td>
+</tr>
+<tr class="odd">
+<td>trinity</td>
+<td>2.6.6</td>
+<td>trinity/2.6</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>Trinity RNA-Seq de novo transcriptome assembly</td>
+</tr>
+<tr class="even">
+<td>ucsc-liftover</td>
+<td>366</td>
+<td>ucsc-liftover/366</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>The Batch Coordinate Conversion (liftOver) utility converts genome coordinates and genome annotation files between assemblies.</td>
+</tr>
+<tr class="odd">
+<td>viennarna</td>
+<td>2.3.3</td>
+<td>viennarna/2.3</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>The ViennaRNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.</td>
+</tr>
+<tr class="even">
+<td>xcrysden</td>
+<td>1.5.60</td>
+<td>xcrysden/1.5</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>physics</td>
+<td>XCrySDen is a crystalline and molecular structure visualisation program aiming at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated.</td>
+</tr>
+<tr class="odd">
+<td>zerone</td>
+<td>1.0</td>
+<td>zerone/1.0</td>
+<td>None<br />
+</td>
+<td>application</td>
+<td>computational biology</td>
+<td>Zerone discretizes several ChIP-seq replicates simultaneously and resolves conflicts between them. After the job is done, Zerone checks the results and tells you whether it passes the quality control.</td>
+</tr>
+</tbody>
+</table>
+
+Attachments:
+------------
+
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+
+Document generated by Confluence on Oct 24, 2018 14:48
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/available_software_for_tusker.md b/content/guides/running_applications/available_software_for_tusker.md
new file mode 100644
index 00000000..75443a68
--- /dev/null
+++ b/content/guides/running_applications/available_software_for_tusker.md
@@ -0,0 +1,2945 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Running Applications](Running-Applications_7471153.html)
+
+<span id="title-text"> HCC-DOCS : Available Software for Tusker </span>
+=======================================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified by
+<span class="editor"> Natasha Pavlovikj</span> on Aug 06, 2018
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-approve confluence-information-macro-icon"></span>
+
+HCC provides some software packages via the Singularity container
+software. If you do not see a desired package in the module list below,
+please check the [Using
+Singularity](https://hcc-docs.unl.edu/display/HCCDOC/Using+Singularity) page
+for the software list there.
+
+Module prerequisites
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-warning confluence-information-macro-icon"></span>
+
+If a module lists one or more prerequisites, the prerequisite module(s)
+must be loaded before or along with, that module.
+
+For example, the `cdo/2.1` modules requires `compiler/pgi/13.` To load
+the cdo module, doing either
+
+`module load compiler/pgi/13module load cdo/2.1`
+
+or
+
+`module load compiler/pgi/13 cdo/2.1` (Note the prerequisite module
+**must** be first.)
+
+is acceptable.
+
+Multiple versions
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-info confluence-information-macro-icon"></span>
+
+Some packages list multiple compilers for prerequisites. This means that
+the package has been built with each version of the compilers listed.
+
+| Name | Version | Module Name | Prerequisite(s) | Type | Domain | Description |
+|------------------------|---------------|----------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-------------|--------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| abacus | 1.0.1 | abacus/1.0 | compiler/intel/13:openmpi/1.8 | library | runtime support | |
+| abinit | 8.0.8 | abinit/8.0 | compiler/intel/12:openmpi/1.8 | application | computational chemistry | ABINIT is a package whose main program allows one to find the total energy. |
+| abyss | 2.1.0 | abyss/2.1 | compiler/gcc/6.1:openmpi/2.1 | application | bioinformatics | ABySS is a de novo sequence assembler intended for short paired-end reads and large genomes. |
+| acml | 5.1 | acml/5.1 | compiler/gcc/4.6 compiler/gcc/4.7 compiler/gcc/4.8 compiler/gcc/4.9 compiler/intel/11 compiler/intel/12 compiler/intel/13 compiler/pgi/11 compiler/pgi/12 compiler/pgi/13 compiler/pgi/14 | library | runtime support | |
+| acml | 5.3 | acml/5.3 | compiler/gcc/4.6 compiler/gcc/4.7 compiler/gcc/4.8 compiler/gcc/4.9 compiler/intel/11 compiler/intel/12 compiler/intel/13 compiler/pgi/11 compiler/pgi/12 compiler/pgi/13 compiler/pgi/14 | library | runtime support | |
+| acml | 6.1 | acml/6.1 | compiler/gcc/4.6 compiler/gcc/4.7 compiler/gcc/4.8 compiler/gcc/4.9 | library | runtime support | |
+| aligngraph | 1.0 | aligngraph/1.0 | None | application | computational biology | |
+| allpathslg | Latest | allpathslg/latest | compiler/gcc/4.7 | application | biology | |
+| anaconda | 2.7 | anaconda/2.7 | None | application | system | |
+| anaconda | 3.3 | anaconda/3.3 | None | application | system | |
+| anaconda | 3.4 | anaconda/3.4 | None | application | system | |
+| anaconda | 4.3 | anaconda/4.3 | None | application | system | |
+| ant | 1.8 | ant/1.8 | None | library | java | |
+| asreml | 3.0 | asreml/3.0 | None | application | data analysis | ASReml |
+| asreml | 4.1 | asreml/4.1 | None | application | data analysis | ASReml |
+| atk | 13.8.2 | atk/13.8.2 | compiler/gcc/4.7:mpich2/1.5 | application | Chemistry | |
+| atk | 2014.1 | atk/2014.1 | compiler/gcc/4.7:mpich2/1.5 | application | Chemistry | |
+| atk | 2015.1 | atk/2015.1 | compiler/gcc/4.7:mpich2/1.5 | application | Chemistry | |
+| augustus | 3.0 | augustus/3.0 | compiler/gcc/4.9 | application | computational biology | AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. |
+| automake | 1.14 | automake/1.14 | None | application | Utilities | Automake is a tool for automatically generating Makefile.in files compliant with the GNU Coding Standards. |
+| automake | 1.15 | automake/1.15 | None | application | Utilities | Automake is a tool for automatically generating Makefile.in files compliant with the GNU Coding Standards. |
+| ballgown | 2.2.0 | ballgown/2.2 | None | application | computational biology | Ballgown is a software package designed to facilitate flexible differential expression analysis of RNA-Seq data. It also provides functions to organize, visualize, and analyze the expression measurements for your transcriptome assembly. |
+| bam-readcount | 0.6 | bam-readcount/0.6 | None | application | computational biology | The purpose of this program is to generate metrics at single nucleotide positions. |
+| bayespeak | 1.24.0 | bayespeak/1.24.0 | None | application | computational biology | This package is an implementation of the BayesPeak algorithm for peak-calling in ChIP-seq data. |
+| bcftools | 1.1 | bcftools/1.1 | compiler/gcc/4.8 | application | computational biology | BCF Tools - a generic tool for the Variant Call Format(VCF) |
+| bcftools | 1.2 | bcftools/1.2 | compiler/gcc/4.8 | application | computational biology | BCF Tools - a generic tool for the Variant Call Format(VCF) |
+| bcl2fastq | 2.17 | bcl2fastq/2.17 | compiler/gcc/4.7 | application | biology | bcl2fastq can be used to demultiplex data and convert BCL files to FASTQ file formats for downstream analysis |
+| BICseq | 1.1.2 | BICseq/1.1 | None | application | computational biology | BIC-seq can accurately and efficiently identify CNVs via minimizing the Bayesian information criterion. |
+| bioperl | 1.6 | bioperl/1.6 | None | application | computational biology | BioPerl is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications |
+| biopieces | 1.0 | biopieces/1.0 | compiler/gcc/4.7:openmpi/1.6 | application | computational biology | The Biopieces are a collection of bioinformatics tools that can be pieced together in a very easy and flexible manner to perform both simple and complex tasks. |
+| biosamtools | 1.38 | biosamtools/1.38 | None | application | computational biology | |
+| bismark | 0.14.2 | bismark/0.14 | None | application | computational biology | Bisulfite read mapper and methylation caller. |
+| bismark | 0.19.0 | bismark/0.19 | None | application | computational biology | Bisulfite read mapper and methylation caller. |
+| blast | 2.2.30 | blast/2.2 | None | application | computational biology | NCBI BLAST+ sequence alignment package. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. |
+| blast | 2.4.0 | blast/2.4 | None | application | computational biology | NCBI BLAST+ sequence alignment package. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. |
+| blast-legacy | 2.2.26 | blast-legacy/2.2.26 | None | application | computational biology | NCBI BLAST sequence alignment package. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. |
+| blat | 34 | blat/34 | None | application | computational biology | Blat is an alignment tool like BLAST, but it is structured differently. On DNA, Blat works by keeping an index of an entire genome in memory. Thus, the target database of BLAT is not a set of GenBank sequences, but instead an index derived from the assembly of the entire genome. |
+| blat | 35x1 | blat/35x1 | None | application | computational biology | Blat is an alignment tool like BLAST, but it is structured differently. On DNA, Blat works by keeping an index of an entire genome in memory. Thus, the target database of BLAT is not a set of GenBank sequences, but instead an index derived from the assembly of the entire genome. |
+| boost | 1.57 | boost/1.57 | compiler/gcc/4.9 | application | System Environment/Base | Boost provides free peer-reviewed portable C++ source libraries. |
+| boost | 1.59 | boost/1.59 | compiler/gcc/4.9 compiler/gcc/5.4 compiler/gcc/6.1 | application | System Environment/Base | Boost provides free peer-reviewed portable C++ source libraries. |
+| boost | 1.61 | boost/1.61 | compiler/intel/13 None | application | System Environment/Base | Boost provides free peer-reviewed portable C++ source libraries. |
+| boost | 1.63 | boost/1.63 | compiler/gcc/6.1 compiler/intel/16 | application | System Environment/Base | Boost provides free peer-reviewed portable C++ source libraries. |
+| boost | 1.64 | boost/1.64 | compiler/gcc/7.1 | application | System Environment/Base | Boost provides free peer-reviewed portable C++ source libraries. |
+| boost | 1.66 | boost/1.66 | compiler/gcc/7.1 compiler/gcc/8.2 | application | System Environment/Base | Boost provides free peer-reviewed portable C++ source libraries. |
+| bowtie | 0.12.8 | bowtie/0.12.8 | None | application | computational biology | Ultrafast, memory-efficient short read aligner |
+| bowtie | 0.12.9 | bowtie/0.12.9 | None | application | computational biology | Ultrafast, memory-efficient short read aligner |
+| bowtie | 1.0.0 | bowtie/1.0.0 | None | application | computational biology | Ultrafast, memory-efficient short read aligner |
+| bowtie | 1.1.2 | bowtie/1.1 | None | application | computational biology | Ultrafast, memory-efficient short read aligner |
+| bowtie | 2.0.0-beta6 | bowtie/2.0.0-beta6 | None | application | computational biology | Ultrafast, memory-efficient short read aligner |
+| bowtie | 2.1.0 | bowtie/2.1.0 | None | application | computational biology | Ultrafast, memory-efficient short read aligner |
+| bowtie | 2.2.6 | bowtie/2.2 | None | application | computational biology | Ultrafast, memory-efficient short read aligner |
+| bowtie | 2.3.4 | bowtie/2.3 | None | application | computational biology | Bowtie2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. |
+| bwa | 0.6.2 | bwa/0.6 | None | application | computational biology | bwa - Burrows-Wheeler Alignment Tool |
+| bwa | 0.7 | bwa/0.7 | None | application | computational biology | bwa - Burrows-Wheeler Alignment Tool |
+| bzip2 | 1.0 | bzip2/1.0 | None | library | runtime support | |
+| canu | 1.6 | canu/1.6 | None | application | computational biology | |
+| cap3 | 122107 | cap3/122107 | None | application | computational biology | CAP3: A DNA Sequence Assembly Program |
+| CAPmiRSEQ | 1.0 | CAPmiRSEQ/1.0 | None | library | runtime support | |
+| cdna-cupcake-tofu2 | 5.2 | cdna-cupcake-tofu2/5.2 | None | application | computational biology | cDNA\_Cupcake is a miscellaneous collection of Python and R scripts used for analyzing sequencing data. |
+| cdo | 1.6 | cdo/1.6 | compiler/gcc/4.7 | library | runtime support | |
+| cexor | 1.10 | cexor/1.10 | None | application | computational biology | An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates. |
+| clark | 1.2.3 | clark/1.2 | None | application | computational biology | |
+| clustal-omega | 1.2 | clustal-omega/1.2 | None | application | computational biology | Clustal Omega is the latest addition to the Clustal family. It offers a significant increase in scalability over previous versions, allowing hundreds of thousands of sequences to be aligned in only a few hours |
+| CNVnator | 0.3 | CNVnator/0.3 | compiler/gcc/4.9 | application | genotyping | CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. |
+| cogent | 3.1 | cogent/3.1 | None | application | computational biology | Cogent is a tool for reconstructing the coding genome using high-quality full-length transcriptome sequences. |
+| cometa | 1.0 | cometa/1.0 | compiler/gcc/4.9:openmpi/1.10 | library | runtime support | |
+| compiler/gcc | 4.6 | compiler/gcc/4.6 | None | application | compiler | |
+| compiler/gcc | 4.7 | compiler/gcc/4.7 | None | application | compiler | |
+| compiler/gcc | 4.8 | compiler/gcc/4.8 | None | application | compiler | |
+| compiler/gcc | 4.9 | compiler/gcc/4.9 | None | application | compiler | |
+| compiler/gcc | 5.4 | compiler/gcc/5.4 | None | application | compiler | |
+| compiler/gcc | 6.1 | compiler/gcc/6.1 | None | application | compiler | |
+| compiler/gcc | 7.1 | compiler/gcc/7.1 | None | application | compiler | |
+| compiler/gcc | 8.2 | compiler/gcc/8.2 | None | application | compiler | |
+| compiler/intel | 11 | compiler/intel/11 | None | application | compiler | |
+| compiler/intel | 12 | compiler/intel/12 | None | application | compiler | |
+| compiler/intel | 13 | compiler/intel/13 | None | application | compiler | |
+| compiler/intel | 15 | compiler/intel/15 | None | application | compiler | |
+| compiler/intel | 16 | compiler/intel/16 | None | application | compiler | |
+| compiler/intel | 18 | compiler/intel/18 | None | application | compiler | |
+| compiler/open64 | 4.5 | compiler/open64/4.5 | None | application | compiler | |
+| compiler/pgi | 11 | compiler/pgi/11 | None | application | compiler | |
+| compiler/pgi | 12 | compiler/pgi/12 | None | application | compiler | |
+| compiler/pgi | 13 | compiler/pgi/13 | None | application | compiler | |
+| compiler/pgi | 14 | compiler/pgi/14 | None | application | compiler | |
+| compiler/pgi | 15 | compiler/pgi/15 | None | application | compiler | |
+| compiler/pgi | 16 | compiler/pgi/16 | None | application | compiler | |
+| cp2k | 2.6 | cp2k/2.6 | compiler/gcc/4.7:openmpi/1.8 | library | runtime support | |
+| cp2k | 3.0 | cp2k/3.0 | compiler/gcc/4.7:openmpi/1.8 | library | runtime support | |
+| cplex | 12.5 | cplex/12.5 | None | library | runtime | CPLEX - High-performance mathematical programming solver for linear programming, mixed integer programming, and quadratic programming. |
+| crest | 1.0 | crest/1.0 | None | application | computational biology | |
+| csaw | 1.4 | csaw/1.4 | None | application | computational biology | Detection of differentially bound regions in ChIP-seq data with sliding windows, with methods for normalization and proper FDR control. |
+| cuda | 5.5 | cuda/5.5 | None | application | compiler | NVIDIA CUDA Toolkit for Linux. |
+| cuda | 6.0 | cuda/6.0 | None | application | compiler | NVIDIA CUDA Toolkit for Linux. |
+| cuda | 6.5 | cuda/6.5 | None | application | compiler | NVIDIA CUDA Toolkit for Linux. |
+| cufflinks | 2.0.2 | cufflinks/2.0.2 | None | application | computational biology | cufflinks - Transcript assembly, differential expression, and differential regulation for RNA-Seq |
+| cufflinks | 2.1.1 | cufflinks/2.1.1 | None | application | computational biology | cufflinks - Transcript assembly, differential expression, and differential regulation for RNA-Seq |
+| cufflinks | 2.2 | cufflinks/2.2 | None | application | computational biology | cufflinks - Transcript assembly, differential expression, and differential regulation for RNA-Seq |
+| curl | 7.50 | curl/7.50 | None | application | network | |
+| dmtcp | 2.0 | dmtcp/2.0 | None | application | Utility | |
+| dmtcp | 2.3 | dmtcp/2.3 | None | application | Utility | |
+| dmtcp | 2.4 | dmtcp/2.4 | None | application | Utility | |
+| dmtcp | 2.5 | dmtcp/2.5 | None | application | Utility | |
+| ea-utils | 1.01 | ea-utils/1.0 | None | application | computational biology | EA Utils is a collection of command line tools for processing NextGen sequencing data. Included are fastq-stats and sam-stats which are lightweight tools that display a variety of statistics on fastq and sam files. |
+| edirect | 1.0 | edirect/1.0 | None | application | unknown | Entrez Direct (EDirect) is an advanced method for accessing the NCBI's set of interconnected databases. |
+| elk | 4.3.6 | elk/4.3 | compiler/intel/13:openmpi/1.8 | library | runtime support | |
+| emacs | 24.5 | emacs/24.5 | None | application | unknown | |
+| emboss | 6.5.7 | emboss/6.5 | None | application | computational biology | EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. |
+| erne | 2.1.1 | erne/2.1 | None | application | computational biology | ERNE is a short string alignment package whose goal is to provide an all-inclusive set of tools to handle short (NGS-like) reads. |
+| espresso | 5.0 | espresso/5.0 | compiler/intel/13:openmpi/1.8 | library | runtime support | |
+| exiv2 | 0.25 | exiv2/0.25 | compiler/gcc/4.9 | library | images | |
+| exomiser | 7.2 | exomiser/7.2 | None | application | computational biology | The Exomiser is a Java program that finds potential disease-causing variants from whole-exome or whole-genome sequencing data. |
+| exonerate | 2.2 | exonerate/2.2 | None | application | computational biology | Exonerate - a generic tool for sequence alignment. |
+| expat | 2.2 | expat/2.2 | compiler/gcc/4.9 | library | xml | |
+| express | 1.5 | express/1.5 | None | application | life sciences | express - Streaming quantification for high-throughput sequencing |
+| fastqc | 0.10 | fastqc/0.10 | None | application | computational biology | fastqc - A Quality Control application for FastQ files |
+| fastx\_toolkit | 0.0.14 | fastx\_toolkit/0.0.14 | None | application | computational biology | FASTX Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. |
+| fftw2 | 2.1 | fftw2/2.1 | compiler/intel/13 | library | runtime support | |
+| fftw3 | 3.3 | fftw3/3.3 | compiler/gcc/4.7 compiler/gcc/4.9 compiler/intel/13 compiler/intel/15 compiler/intel/16 | library | runtime support | |
+| flash | 1.2.11 | flash/1.2 | compiler/gcc/4.9 | application | computational biology | FLASH (Fast Length Adjustment of SHort reads) is a very fast and accurate software tool to merge paired-end reads from next-generation sequencing experiments. FLASH is designed to merge pairs of reads when the original DNA fragments are shorter than twice the length of reads. The resulting longer reads can significantly improve genome assemblies. They can also improve transcriptome assembly when FLASH is used to merge RNA-seq data. |
+| gamess | 20141205R1 | gamess/20141205R1 | compiler/intel/13:openmpi/1.8 | library | runtime support | |
+| gap | 4.5 | gap/4.5 | None | library | runtime | GAP is a system for computational discrete algebra, with particular emphasis on Computational Group Theory. |
+| gatk | 3.4-46 | gatk/3.4 | None | application | computational biology | The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyze high-throughput sequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size. |
+| gdal | 1.11 | gdal/1.11 | compiler/gcc/4.7 | library | runtime support | |
+| gdcclient | 1.2.0 | gdcclient/1.2 | compiler/gcc/4.9 | library | runtime support | |
+| gdl | 0.9 | gdl/0.9 | None | library | runtime | |
+| genemarks | 2.5p | genemarks/2.5p | None | application | computational biology | GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions |
+| genemarks | 4.3 | genemarks/4.3 | None | application | computational biology | GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions |
+| genewise | 2.4 | genewise/2.4 | None | application | computational biology | The Wise2 form compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors. |
+| geos | 3.5 | geos/3.5 | compiler/gcc/4.7 compiler/gcc/4.9 | library | runtime support | |
+| gromacs | 4.6 | gromacs/4.6 | compiler/gcc/4.7:openmpi/1.6 | library | runtime support | |
+| gromacs | 5.1.4 | gromacs/5.1 | compiler/gcc/4.8:openmpi/1.8 | application | computational biology | GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. |
+| GSL | 1.16 | GSL/1.16 | compiler/gcc/4.9 | library | runtime support | |
+| GSL | 2.1 | GSL/2.1 | compiler/gcc/4.9 | library | runtime support | |
+| gtool | 0.7.5 | gtool/0.7 | compiler/gcc/6.1 | application | computational biology | GTOOL is a program for transforming sets of genotype data for use with the programs SNPTEST and IMPUTE. |
+| hapflk | 1.3.0 | hapflk/1.3 | None | application | package | hapflk is a software implementing the hapFLK \[1\] and FLK \[2\] tests for the detection of selection signatures based on multiple population genotyping data. |
+| hdf4 | 4.2 | hdf4/4.2 | compiler/gcc/4.7 compiler/intel/11 compiler/intel/12 compiler/pgi/11 compiler/pgi/12 compiler/pgi/15 | library | runtime support | |
+| hdf5 | 1.8 | hdf5/1.8 | compiler/gcc/4.7 compiler/gcc/4.8 compiler/gcc/4.9 compiler/intel/11 compiler/intel/12 compiler/intel/13 compiler/intel/15 compiler/pgi/11 compiler/pgi/12 compiler/pgi/13 compiler/pgi/14 compiler/pgi/15 | library | runtime support | |
+| hdf5 | 1.8.6 | hdf5/1.8.6 | compiler/intel/12 compiler/pgi/11 | library | runtime support | |
+| hdfeos2 | 2.18 | hdfeos2/2.18 | compiler/gcc/4.7 compiler/intel/11 compiler/intel/12 compiler/pgi/11 compiler/pgi/12 | library | runtime support | |
+| hdfeos5 | 1.14 | hdfeos5/1.14 | compiler/gcc/4.7 compiler/intel/11 compiler/intel/12 compiler/pgi/11 compiler/pgi/12 | library | runtime support | |
+| hiddendomains | 2.3 | hiddendomains/2.3 | None | application | chip-seq | hiddenDomains is a suite of programs used to identify significant enrichment of ChIP-seq reads that span large domains. |
+| hisat2 | 2.0.5 | hisat2/2.0 | None | application | computational biology | HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). |
+| hmmer | 3.1 | hmmer/3.1 | compiler/gcc/4.7:openmpi/1.6 compiler/gcc/4.9:openmpi/1.8 | application | computational biology | HMMER biosequence analysis using profile hidden Markov models |
+| hmmer | 3.1b2 | hmmer/3.1 | compiler/gcc/4.8:openmpi/1.8 | application | computational biology | HMMER biosequence analysis using profile hidden Markov models |
+| HTSeq | 0.5.4p5 | HTSeq/0.5.4p5 | None | application | computational biology | HTSeq - Analysing high-throughput sequencing data with Python |
+| HTSeq | 0.6.1p1 | HTSeq/0.6.1p1 | None | application | computational biology | HTSeq - Analysing high-throughput sequencing data with Python |
+| htslib | 1.3.2 | htslib/1.3 | None | application | computational biology | HTSlib is an implementation of a unified C library for accessing common file formats. |
+| HTSlib | 1.2 | HTSlib/1.2 | compiler/gcc/4.8 | application | computational biology | HTSlib - the core library used by samtools and bcftools. |
+| hugeseq | 1.0 | hugeseq/1.0 | None | application | computational biology | HugeSeq is a fully integrated system for genome analysis from mapping reads to the identification and annotation of all types of variants: SNPS, Indels and SVs. |
+| humann2 | 0.9.9 | humann2/0.9 | None | application | computational biology | HUMAnN2 is the next generation of HUMAnN (HMP Unified Metabolic Analysis Network). |
+| idba | 1.1.3 | idba/1.1 | None | application | computational biology | IDBA is a practical iterative De Bruijn Graph De Novo Assembler for sequence assembly in bioinfomatics. |
+| idr | 2.0 | idr/2.0 | None | application | computational biology | The IDR (Irreproducible Discovery Rate) framework is a uni�ed approach to measure the reproducibility of �ndings identi�ed from replicate experiments and provide highly stable thresholds based on reproducibility. |
+| ijg-libjpeg | 9b | ijg-libjpeg/9b | compiler/gcc/4.9 | library | images | |
+| ilmbase | 2.2 | ilmbase/2.2 | compiler/gcc/4.9 | library | images | |
+| ima2p | 1.0 | ima2p/1.0 | compiler/gcc/4.9:openmpi/1.10 | application | Bayesian MCMC | IMa2p is a parallel implementation of IMa2, using OpenMPI-C++ - a Bayesian MCMC based method for inferring population demography under the IM (Isolation with Migration) model. |
+| imagemagick | 5.5 | imagemagick/5.5 | compiler/gcc/4.7 | library | image editing | ImageMagick® is a software suite to create, edit, compose, or convert bitmap images. |
+| imagemagick | 6.8 | imagemagick/6.8 | compiler/gcc/4.7 | library | image editing | ImageMagick® is a software suite to create, edit, compose, or convert bitmap images. |
+| intel-mkl | 12 | intel-mkl/11 | None None | library | tools | Numerical library, contains blas/lapack |
+| intel-mkl | 13 | intel-mkl/13 | None | library | tools | Numerical library, contains blas/lapack |
+| intel-mkl | 15 | intel-mkl/15 | None | library | tools | Numerical library, contains blas/lapack |
+| intel-mkl | 16 | intel-mkl/16 | None | library | tools | Numerical library, contains blas/lapack |
+| interproscan | 5.23-62.0 | interproscan/5.23 | compiler/gcc/4.8 | application | computational biology | Scans a range of protein signatures against your sequences and provides protein functional analysis. |
+| interproscan | 5.24-63.0 | interproscan/5.24 | compiler/gcc/4.8 | application | computational biology | Scans a range of protein signatures against your sequences and provides protein functional analysis. |
+| interproscan | 5.8-49.0 | interproscan/5.8 | None | application | computational biology | Scans a range of protein signatures against your sequences and provides protein functional analysis. |
+| irods | 4.1 | irods/4.1 | None | application | unknown | The integrated Rule-Oriented Data System (iRODS) is open source data management software used by research organizations and government agencies worldwide. This module includes the icommands client programs only. |
+| jags | 3.4 | jags/3.4 | compiler/gcc/4.9 | application | mathematics | JAGS is Just Another Gibbs Sampler. |
+| jags | 4.2 | jags/4.2 | compiler/gcc/4.9 | application | mathematics | JAGS is Just Another Gibbs Sampler. |
+| jellyfish | 2.2.0 | jellyfish/2.2 | None | application | computational biology | Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. |
+| jellyfish | 2.2.7 | jellyfish/2.2 | compiler/gcc/4.9 | application | computational biology | Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. |
+| jmosaics | 1.10 | jmosaics/1.10 | None | application | computational biology | Joint analysis of multiple ChIP-Seq data sets. |
+| julia | 0.6.2 | julia/0.6 | None | application | Language | Julia is a high-level, high-performance dynamic programming language for numerical computing. |
+| kaiju | 1.4.4 | kaiju/1.4 | compiler/gcc/4.9 | library | runtime support | |
+| kaiju | 1.5.0 | kaiju/1.5 | compiler/gcc/4.9 | application | Bioinformatics | |
+| kalign | 2.03 | kalign/2.03 | None | application | computational biology | Kalign is a fast and accurate multiple sequence alignment algorithm designed to align large numbers of protein sequences. |
+| kallisto | 0.42.3 | kallisto/0.42 | compiler/gcc/4.8 | library | runtime support | |
+| khmer | 2.0 | khmer/2.0 | None | application | computational biology | Khmer is tools for in-memory nucleotide sequence k-mer counting, filtering, graph traversal and more. |
+| kraken | 1.0 | kraken/1.0 | None | application | computational biology | Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. |
+| lammps | 10Aug15 | lammps/10Aug15 | compiler/intel/15:openmpi/1.8 | library | runtime support | |
+| lammps | 10Feb2017 | lammps/10Feb2017 | compiler/gcc/6.1:openmpi/2.0 | library | runtime support | |
+| lammps | 15May15 | lammps/15May15 | compiler/gcc/4.9:openmpi/1.8 compiler/gcc/4.9:openmpi/2.1 | library | runtime support | |
+| lammps | 16Aug13 | lammps/16Aug13 | compiler/gcc/4.7:openmpi/1.6 | library | runtime support | |
+| lammps | 30Oct14 | lammps/30Oct14 | compiler/gcc/4.8:openmpi/1.8 | library | runtime support | |
+| libint | 1.1 | libint/1.1 | compiler/gcc/4.7 | application | Computational Chemistry | Libint is a software stack for computing integrals used in molecular quantum mechanics |
+| libraw | 0.17 | libraw/0.17 | compiler/gcc/4.9 | library | images | |
+| libtiff | 4.0 | libtiff/4.0 | compiler/gcc/4.9 | library | images | |
+| libxc | 2.2.3 | libxc/2.2 | compiler/intel/13 | library | runtime support | |
+| libxml2 | 2.9 | libxml2/2.9 | compiler/gcc/4.9 | library | runtime support | |
+| libxslt | 1.1 | libxslt/1.1 | compiler/gcc/4.9 | library | runtime support | |
+| lofreq | 2.1.3.1 | lofreq/2.1 | None | application | computational biology | LoFreq is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. |
+| lsdyna | 10.0 | lsdyna/10.0 | None | application | unknown | |
+| lsdyna | 10.1 | lsdyna/10.1 | None | application | unknown | |
+| lsdyna | 6.0.0 | lsdyna/6.0.0 | None | application | unknown | |
+| lsdyna | 6.1.2 | lsdyna/6.1.2 | None | application | unknown | |
+| lsdyna | 7.0.0 | lsdyna/7.0.0 | None | application | unknown | |
+| lsdyna | 7.1.1 | lsdyna/7.1.1 | None | application | unknown | |
+| lsdyna | 8.0.0 | lsdyna/8.0.0 | None | application | unknown | |
+| lsdyna | 8.0.1 | lsdyna/8.0.1 | None | application | unknown | |
+| lsdyna | 8.1.0 | lsdyna/8.1.0 | None | application | unknown | |
+| lsdyna | 9.0.1 | lsdyna/9.0.1 | None | application | unknown | |
+| lsdyna | 9.2.0 | lsdyna/9.2.0 | None | application | unknown | |
+| luminance-hdr | 2.4 | luminance-hdr/2.4 | compiler/gcc/4.9 | library | image | |
+| m4 | 1.4 | m4/1.4 | None | application | Utilities | GNU M4 is an implementation of the traditional Unix macro processor. |
+| mach | 1.0.18 | mach/1.0 | compiler/gcc/4.8 | library | runtime support | |
+| mafft | 7.1 | mafft/7.1 | compiler/gcc/4.8 | application | computational biology | MAFFT - a generic tool for sequence alingments. |
+| maq | 0.7 | maq/0.7 | None | application | computational biology | maq - Mapping and Assembly with Quality. |
+| mauve | 2.4 | mauve/2.4 | None | application | computational biology | mauve - Multiple Genome Alignment. |
+| maven | 3.2 | maven/3.2 | None | application | system | Apache Maven is a software project management and comprehension tool. |
+| maven | 3.5 | maven/3.5 | None | application | system | Apache Maven is a software project management and comprehension tool. |
+| meerkat | 0.189 | meerkat/0.1 | None | application | computational biology | Meerkat is designed to identify structural variations |
+| MEME | 4.11.3 | MEME/4.11 | None | application | computational biology | The MEME suite is a collection of tools for the discovery and analysis of sequence motifs. It is hosted at http://meme-suite.org/. |
+| meme-suite | 4.12.0 | meme-suite/4.12 | compiler/gcc/6.1:openmpi/2.0 | application | computational biology | |
+| metacluster | 1.2 | metacluster/1.2 | compiler/gcc/4.9:openmpi/1.10 | library | runtime support | |
+| metaphlan | 1.7 | metaphlan/1.7 | None | application | computational biology | MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. |
+| metaphlan | 2.6.0 | metaphlan/2.6 | None | application | metagenomic phylogenetic analysis | MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. |
+| metavelvet | 1.2.01 | metavelvet/1.2 | None | application | computational biology | MetaVelvet is an extension of Velvet assembler to de novo metagenome assembly from short sequence reads. |
+| mongodb-client | 3.2 | mongodb-client/3.2 | None | application | Utility | Client programs for MongoDB. |
+| mongodb-client | 3.4 | mongodb-client/3.4 | None | application | Utility | Client programs for MongoDB. |
+| mono | 4.6 | mono/4.6 | None | application | compiler | Mono is an open source implementation of Microsoft's .NET Framework based on the ECMA standards for C\# and the Common Language Runtime. |
+| mono | 5.10 | mono/5.10 | None | application | compiler | Mono is an open source implementation of Microsoft's .NET Framework based on the ECMA standards for C\# and the Common Language Runtime. |
+| mosaik | 2.2 | mosaik/2.2 | None | application | computational biology | MOSAIK is a reference-guided aligner for next-generation sequencing technologies. |
+| mothur | 1.35.1 | mothur/1.35 | compiler/gcc/4.9:openmpi/1.8 | library | runtime support | |
+| mpich2 | 1.5 | mpich2/1.5 | compiler/gcc/4.7 | library | runtime support | |
+| mplus | 6.12 | mplus/6.12 | None | application | unknown | Mplus is a latent variable modeling program with a wide variety of analysis capabilities. |
+| mplus | 7.0 | mplus/7.0 | None | application | unknown | Mplus is a latent variable modeling program with a wide variety of analysis capabilities. |
+| mrbayes | 3.2 | mrbayes/3.2 | compiler/gcc/4.8 | application | computational biology | MrBayes - a generic tool for phylogenetic analysis. |
+| mugsy | v1r2.3 | mugsy/v1r2.3 | None | application | computational biology | |
+| multiqc | 0.8 | multiqc/0.8 | None | application | computational biology | Aggregate results from bioinformatics analyses across many samples into a single report |
+| multiwell | 2017 | multiwell/2017 | compiler/gcc/6.1:openmpi/2.1 | application | chemistry | MultiWell calculates time dependent concentrations, reaction yields, vibrational distributions, and rate constants as functions of temperature and pressure for multi-well, multi-channel unimolecular reactions systems that consist of stable species and multiple isomerization and/or dissociation reactions. |
+| mummer | 3.23 | mummer/3.23 | None | application | computational biology | MUMmer - A modular system for the rapid whole genome alignment of finished or draft sequence |
+| muscle | 3.8 | muscle/3.8 | None | application | computational biology | Popular multiple alignment software |
+| music | 1.0 | music/1.0 | None | application | computational biology | MUSIC is an algorithm for identification of enriched regions at multiple scales in the read depth signals from ChIP-Seq experiments. |
+| mutect | 1.1 | mutect/1.1 | None | application | computational biology | MuTect is a method developed at the Broad Institute for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes. |
+| mytaxa | 1.0 | mytaxa/1.0 | None | application | computational biology | MyTaxa - Assign taxonomy to metagenomic fragments. |
+| NCL | 6.0 | NCL/6.0 | compiler/pgi/11 None | application | utility | A library of graphics utilites from the Natl. Center for Atmospheric Research. |
+| NCL | 6.1 | NCL/6.1dist | None | application | utility | A library of graphics utilites from the Natl. Center for Atmospheric Research. |
+| NCL | 6.3 | NCL/6.3 | None | application | utility | A library of graphics utilites from the Natl. Center for Atmospheric Research. |
+| NCL | 6.4 | NCL/6.4 | None | application | utility | A library of graphics utilites from the Natl. Center for Atmospheric Research. |
+| NCO | 4.1 | NCO/4.1 | compiler/pgi/11 | library | runtime support | |
+| NCO | 4.4 | NCO/4.4 | compiler/gcc/4.7 compiler/gcc/4.8 compiler/intel/11 compiler/intel/12 compiler/intel/13 compiler/pgi/12 compiler/pgi/13 compiler/pgi/14 | library | runtime support | |
+| NCO | 4.5 | NCO/4.5 | compiler/gcc/4.7 compiler/gcc/4.8 compiler/gcc/4.9 compiler/intel/11 compiler/intel/12 compiler/intel/13 compiler/intel/15 compiler/pgi/12 compiler/pgi/13 compiler/pgi/14 compiler/pgi/15 | library | runtime support | |
+| netcdf | 4.1 | netcdf/4.1 | compiler/gcc/4.7 compiler/pgi/11 | library | runtime support | |
+| netcdf | 4.2 | netcdf/4.2 | compiler/gcc/4.7 compiler/gcc/4.8 compiler/intel/11 compiler/intel/12 compiler/intel/13 compiler/pgi/11 compiler/pgi/12 compiler/pgi/13 compiler/pgi/14 | library | runtime support | |
+| netcdf | 4.4 | netcdf/4.4 | compiler/gcc/4.7 compiler/gcc/4.8 compiler/gcc/4.9 compiler/intel/11 compiler/intel/12 compiler/intel/13 compiler/intel/15 compiler/pgi/11 compiler/pgi/12 compiler/pgi/13 compiler/pgi/14 compiler/pgi/15 | library | runtime support | |
+| netsurfp | 1.0c | netsurfp/1.0 | None | application | computational biology | NetSurfP predicts the surface accessibility and secondary structure of amino acids in an amino acid sequence. The method also simultaneously predicts the reliability for each prediction, in the form of a Z-score. The Z-score is related to the surface prediction, and not the secondary structure. |
+| nwchem | 6.5 | nwchem/6.5 | compiler/intel/13:openmpi/1.8 | library | runtime support | |
+| nwchem | 6.6 | nwchem/6.6 | compiler/intel/13:openmpi/1.8 | library | runtime support | |
+| nxtrim | 0.3.1 | nxtrim/0.3 | None | application | computational biology | nxtrim: Software to remove Nextera Mate Pair adapters and categorise reads according to the orientation implied by the adapter location. |
+| oases | 0.2.8 | oases/0.2.8 | None | application | computational biology | Oases - De novo transcriptome assembler for very short reads. |
+| openbugs | 3.2 | openbugs/3.2 | None | application | statistics | BUGS is a software package for performing Bayesian inference Using Gibbs Sampling. |
+| opencv | 3.1.0 | opencv/3.1 | None | library | unknown | If the library finds Intel's Integrated Performance Primitives on the system, it will use these proprietary optimized routines to accelerate itself. |
+| openexr | 2.2 | openexr/2.2 | compiler/gcc/4.9 | library | images | |
+| openmpi | 1.10 | openmpi/1.10 | compiler/intel/16 | library | runtime support | |
+| openmpi | 1.10.2 | openmpi/1.10 | compiler/gcc/4.7 compiler/gcc/4.8 compiler/gcc/4.9 compiler/intel/11 compiler/intel/12 compiler/intel/13 compiler/intel/15 compiler/pgi/11 compiler/pgi/12 compiler/pgi/13 compiler/pgi/14 compiler/pgi/15 | library | runtime support | |
+| openmpi | 1.10.6 | openmpi/1.10 | compiler/gcc/5.4 compiler/gcc/6.1 | library | runtime support | |
+| openmpi | 1.6 | openmpi/1.6 | compiler/gcc/4.6 compiler/gcc/4.7 compiler/gcc/4.7 compiler/gcc/4.8 compiler/gcc/4.9 compiler/intel/11 compiler/intel/12 compiler/intel/13 compiler/intel/15 compiler/open64/4.5 compiler/pgi/11 compiler/pgi/12 compiler/pgi/13 compiler/pgi/14 compiler/pgi/15 | library | runtime support | |
+| openmpi | 1.8 | openmpi/1.8 | compiler/gcc/4.7 compiler/gcc/4.8 compiler/gcc/4.9 compiler/intel/11 compiler/intel/12 compiler/intel/13 compiler/intel/15 compiler/pgi/11 compiler/pgi/12 compiler/pgi/13 compiler/pgi/14 compiler/pgi/15 | library | runtime support | |
+| openmpi | 2.0 | openmpi/2.0 | compiler/intel/11 compiler/intel/12 compiler/intel/13 compiler/intel/15 compiler/intel/16 compiler/pgi/11 compiler/pgi/12 compiler/pgi/13 compiler/pgi/14 compiler/pgi/15 | library | runtime support | |
+| openmpi | 2.0.1 | openmpi/2.0 | compiler/gcc/4.7 compiler/gcc/4.8 compiler/gcc/4.9 compiler/gcc/5.4 compiler/gcc/6.1 | library | runtime support | |
+| openmpi | 2.1 | openmpi/2.1 | compiler/intel/12 compiler/intel/13 compiler/intel/15 compiler/intel/16 compiler/pgi/11 compiler/pgi/12 compiler/pgi/13 compiler/pgi/14 compiler/pgi/15 | library | runtime support | |
+| openmpi | 2.1.1 | openmpi/2.1 | compiler/gcc/4.7 compiler/gcc/4.8 compiler/gcc/4.9 compiler/gcc/5.4 compiler/gcc/6.1 | library | runtime support | |
+| openmx | 3.7 | openmx/3.7 | compiler/intel/13:openmpi/1.8 | library | runtime support | |
+| p7zip | 16.02 | p7zip/16.02 | None | application | compression | p7zip is a port of 7za.exe for POSIX systems. |
+| pandaseq | 2.9 | pandaseq/2.9 | compiler/gcc/4.9 | application | bioinforomatics | PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence. |
+| pbh5tools | 0.8.0 | pbh5tools/0.8 | None | application | computational biology | pbh5tools -- tools for manipulating HDF5 files produced by Pacific Biosciences. Specifically, this package provides functionality for manipulating and extracting data from "cmp.h5" and "bas.h5" files. |
+| pblat | 2.0 | pblat/2.0 | None | application | computational biology | |
+| perl-mongodb | 1.2.2 | perl-mongodb/1.2 | None | application | Utility | This is the official Perl driver for MongoDB. |
+| phdf5 | 1.8 | phdf5/1.8 | compiler/gcc/4.7:openmpi/1.6 | library | runtime support | |
+| phdf5 | 1.8.12 | phdf5/1.8 | compiler/gcc/4.8:openmpi/1.8 compiler/pgi/12:openmpi/1.8 compiler/pgi/14:openmpi/1.8 | library | runtime support | |
+| phdf5 | 1.8.13 | phdf5/1.8 | compiler/gcc/4.7:openmpi/1.8 compiler/intel/12:openmpi/1.8 compiler/pgi/11:openmpi/1.8 | library | runtime support | |
+| phobius | 1.01 | phobius/1.01 | None | application | computational biology | Phobius is a combined transmembrane topology and signal peptide predictor. |
+| phonopy | 1.11.12 | phonopy/1.11 | None | library | runtime support | |
+| phrap | 0.990329 | phrap/0.9 | compiler/gcc/4.8 | application | computational biology | Phrap is a program for assembling shotgun DNA sequence data. Cross\_match is a general purpose utility for comparing any two DNA sequence sets using a 'banded' version of swat. Swat is a program for searching one or more DNA or protein query sequences, or a query profile, against a sequence database, using an efficient implementation of the Smith-Waterman or Needleman-Wunsch algorithms with linear (affine) gap penalties. |
+| phylip | 3.696 | phylip/3.696 | compiler/gcc/4.9 | application | computational biology | PHYLIP (the PHYLogeny Inference Package) is a package of programs for inferring phylogenies (evolutionary trees). |
+| phymmbl | 4.0 | phymmbl/4.0 | None | application | computational biology | PhymmBL - Taxonomic Classification of Metagenomic Short Reads. |
+| picard | 1.139 | picard/1.1 | None | application | computational biology | A set of Java command line tools for manipulating high-throughput sequencing data (HTS) data and formats. |
+| picrust | 1.1.0 | picrust/1.1 | None | application | metagenomic | The PICRUSt project aims to support prediction of the unobserved character states in a community of organisms from phylogenetic information about the organisms in that community. |
+| plink | 1.0.2 | plink/1.0 | None | application | computational biology | PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. |
+| plplot | 5.9 | plplot/5.9 | compiler/gcc/4.7 | library | plotting | PLplot is a cross-platform software package for creating scientific plots. |
+| pnetcdf | 4.2 | pnetcdf/4.2 | compiler/pgi/11:openmpi/1.6 compiler/pgi/11:openmpi/1.8 | library | runtime support | |
+| primer3 | 2.3.7 | primer3/2.3 | None | application | computational biology | Primer3 picks primers for PCR reactions |
+| prinseq-lite | 0.20.4 | prinseq-lite/0.20 | None | application | computational biology | PRINSEQ can be used to filter, reformat, or trim your genomic and metagenomic sequence data. |
+| prodigal | 2.60 | prodigal/2.60 | None | application | computational biology | Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee. |
+| prohlatype | 0.9.0 | prohlatype/0.9 | None | application | Computational Biology | This project provides a set of tools to calculate the full posterior distribution of HLA types given read data. |
+| proj | 4.9 | proj/4.9 | compiler/gcc/4.7 | library | runtime support | |
+| pslib | 0.4 | pslib/0.4 | compiler/gcc/4.7 | library | graphics | pslib is a C-library to create PostScript files on the fly. |
+| pymagic | 0.1 | pymagic/0.1 | None | application | computational biology | MAGIC: A diffusion-based imputation method reveals gene-gene interactions in single-cell RNA-sequencing data. |
+| pymeteo | 0.5 | pymeteo/0.5 | None | application | geoscience | General meteorological routines, skew-T/log-p plotting and working with CM1 model data. |
+| python | 3.3 | python/3.3 | None | application | system | |
+| python-openstackclient | 2.1.0 | python-openstackclient/2.1 | None | application | Utility | OpenStackClient (aka OSC) is a command-line client for OpenStack that brings the command set for Compute, Identity, Image, Object Store and Block Storage APIs together in a single shell with a uniform command structure. |
+| qctool | 1.4 | qctool/1.4 | None | application | computational biology | QCTOOL is a command-line utility program for basic quality control of gwas datasets. |
+| qiime | 1.7 | qiime/1.7 | None | application | computational biology | QIIME is an open source software package for comparison and analysis of microbial communities, primarily based on high-throughput amplicon sequencing data (such as SSU rRNA) generated on a variety of platforms, but also supporting analysis of other types of data (such as shotgun metagenomic data). |
+| qiime | 1.9 | qiime/1.9 | None | application | computational biology | QIIME is an open source software package for comparison and analysis of microbial communities, primarily based on high-throughput amplicon sequencing data (such as SSU rRNA) generated on a variety of platforms, but also supporting analysis of other types of data (such as shotgun metagenomic data). |
+| qiime | 2017.9 | qiime/2.0 | None | application | computational biology | QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency. |
+| qiime2 | 2017.9 | qiime2/2017.9 | None | application | computational biology | QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency. |
+| qiime2 | 2018.2 | qiime2/2018.2 | None | application | computational biology | QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency. |
+| quast | 4.1 | quast/4.1 | None | application | computational biology | QUAST. the QUality ASsessment Tool for genome assemblies. |
+| R | 2.15 | R/2.15 | None | library | runtime support | |
+| R | 3.0 | R/3.0 | None | library | runtime support | |
+| R | 3.1 | R/3.1 | None | library | runtime support | |
+| R | 3.2 | R/3.2 | None | library | runtime support | |
+| R | 3.3 | R/3.3 | None | library | runtime support | |
+| RAPSearch2 | 2.19 | RAPSearch2/2.19 | None | application | computational biology | RAPSearch2 is a tool for fast protein similarity searches. |
+| RAxML | 8.1 | RAxML/8.1 | compiler/gcc/4.8 | application | computational biology | RAxML - a generic tool for phylogenetic analysis. |
+| ray | 2.3 | ray/2.3 | compiler/gcc/4.7:openmpi/1.6 compiler/gcc/4.7:openmpi/1.8 | application | computational biology | Ray -- Parallel genome assemblies for parallel DNA sequencing. |
+| repeatmasker | 4.0 | repeatmasker/4.0 | None | application | computational biology | RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. |
+| rmblast | 2.28 | rmblast/2.28 | compiler/gcc/4.8 | application | computational biology | RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST suite. The primary difference between this distribution and the NCBI distribution is the addition of a new program 'rmblastn' for use with RepeatMasker and RepeatModeler. |
+| root | 6.06.08 | root/6.06 | compiler/gcc/4.9 | application | big data | It provides all the functionalities needed to deal with big data processing, statistical analysis, visualisation and storage. |
+| rosetta | 3.8 | rosetta/3.8 | compiler/gcc/4.8:openmpi/1.8 | application | computational biology | The Rosetta software suite includes algorithms for computational modeling and analysis of protein structures. It has enabled notable scientific advances in computational biology, including de novo protein design, enzyme design, ligand docking, and structure prediction of biological macromolecules and macromolecular complexes. |
+| r-scimpute | 0.0.5 | r-scimpute/0.0.5 | None | application | biology | scImpute is accurate and robust imputation of single-cell RNA sequencing data. |
+| rsem | 1.2 | rsem/1.2 | None | application | computational biology | RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. |
+| ruby | 2.1 | ruby/2.1 | None | application | system | |
+| sage | 6.3 | sage/6.3 | None | application | mathematics | 'Sage is a free open-source mathematics software system licensed under the GPL. It builds on top of many existing open-source packages: NumPy, SciPy, matplotlib, Sympy, Maxima, GAP, FLINT, R and many more.' Mission: 'Creating a viable free open source alternative to Magma, Maple, Mathematica and Matlab.' |
+| sage | 8.0 | sage/8.0 | compiler/gcc/5.4 | application | mathematics | 'Sage is a free open-source mathematics software system licensed under the GPL. It builds on top of many existing open-source packages: NumPy, SciPy, matplotlib, Sympy, Maxima, GAP, FLINT, R and many more.' Mission: 'Creating a viable free open source alternative to Magma, Maple, Mathematica and Matlab.' |
+| samtools | 0.1 | samtools/0.1 | None | application | computational biology | SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. |
+| samtools | 1.1 | samtools/1.1 | compiler/gcc/4.8 | application | computational biology | SAM Tools - a generic tool for the sam format alignments. |
+| samtools | 1.2 | samtools/1.2 | compiler/gcc/4.8 | application | computational biology | SAM Tools - a generic tool for the sam format alignments. |
+| samtools | 1.3.1 | samtools/1.3 | None | application | computational biology | SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. |
+| scan-for-matches | 1.0 | scan-for-matches/1.0 | None | application | computational biology | scan\_for\_matches is a utility written in C for locating patterns in DNA or protein FASTA files. |
+| scip | 4.0.0 | scip/4.0 | None | application | constraint integer programming | SCIP is currently one of the fastest non-commercial solvers for mixed integer programming (MIP) and mixed integer nonlinear programming (MINLP). |
+| scythe | 0.991 | scythe/0.991 | None | application | computational biology | Scythe - A Bayesian adapter trimmer. |
+| sga | 0.10 | sga/0.10 | None | application | computational biology | SGA is a de novo assembler designed to assemble large genomes from high coverage short read data. |
+| shengbte | 1.1.1 | shengbte/1.1 | compiler/gcc/4.9:openmpi/1.10 | library | runtime support | |
+| shrimp | 2.2 | shrimp/2.2 | None | application | computational biology | SHRiMP is a software package for aligning genomic reads against a target genome. |
+| shtns | 2.8 | shtns/2.6 | compiler/intel/13 compiler/intel/15 | application | math | |
+| sickle | 1.2 | sickle/1.2 | None | application | computational biology | A windowed adaptive trimming tool for FASTQ files using quality |
+| siesta | 4.1.3 | siesta/4.1 | compiler/gcc/4.9:openmpi/1.10 compiler/intel/13:openmpi/1.8 | library | runtime support | |
+| signalp | 4.1 | signalp/4.1 | None | application | computational biology | signalp predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive bacteria, Gram-negative bacteria, and eukaryotes. |
+| simrna | 3.20 | simrna/3.20 | None | application | computational biology | SimRNA is a tool for simulations of RNA conformational dynamics |
+| smrtlink | 5.0.1 | smrtlink/5.0 | None | application | biology | PacBio’s open-source SMRT Analysis software suite is designed for use with Single Molecule, Real-Time (SMRT) Sequencing data. |
+| smrtlink | 5.1.0 | smrtlink/5.1 | None | application | biology | PacBio’s open-source SMRT Analysis software suite is designed for use with Single Molecule, Real-Time (SMRT) Sequencing data. |
+| snap | 2013.11 | snap/2013.11 | None | application | computational biology | Semi-HMM-based Nucleic Acid Parser gene prediction tool |
+| snp-pipeline | 0.6 | snp-pipeline/0.6 | None | application | computational biology | SNP Pipeline is a pipeline for the production of SNP matrices from sequence data used in the phylogenetic analysis of pathogenic organisms sequenced from samples of interest to food safety. |
+| snptest | 2.5.2 | snptest/2.5 | None | application | computational biology | SNPTEST is a program for the analysis of single SNP association in genome-wide studies. |
+| soapdenovo2 | r240 | soapdenovo2/r240 | None | application | computational biology | soapdenovo2 - novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes |
+| spglib | 1.9.9 | spglib/1.9 | compiler/gcc/4.9 | library | runtime support | |
+| spider | 2.0 | spider/2.0 | None | application | computational biology | Sequence-based Prediction of Local and Nonlocal Structural Features for Proteins. |
+| spp | 1.11 | spp/1.11 | None | application | computational biology | ChIP-seq peak caller |
+| spp | 1.13 | spp/1.13 | None | application | computational biology | ChIP-seq peak caller |
+| SRAtoolkit | 2.3 | SRAtoolkit/2.3 | None | application | computational biology | SRA Toolkit |
+| SRAtoolkit | 2.8 | SRAtoolkit/2.8 | None | application | computational biology | SRA Toolkit |
+| SRAtoolkit | 2.9 | SRAtoolkit/2.9 | None | application | computational biology | The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. |
+| star | 2.5.3a | star/2.5 | compiler/gcc/4.9 | application | biology | Spliced Transcripts Alignment to a Reference |
+| starccm | 10.01.010 | starccm/10.06 | None | library | runtime support | |
+| starccm | 9.01.011 | starccm/9.06 | None | library | runtime support | |
+| StringTie | 1.3.0 | StringTie/1.3 | None | application | computational biology | StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. |
+| structure | 2.3 | structure/2.3 | None | application | computational biology | The program structure is a free software package for using multi-locus genotype data to investigate population structure. |
+| szip | 2.1 | szip/2.1 | compiler/gcc/4.7 compiler/gcc/4.8 compiler/gcc/4.9 compiler/intel/11 compiler/intel/12 compiler/intel/13 compiler/intel/15 compiler/open64/4.5 compiler/pgi/11 compiler/pgi/12 compiler/pgi/13 compiler/pgi/14 compiler/pgi/15 | library | runtime support | |
+| tabix | 0.2 | tabix/0.2 | None | application | computational biology | Tabix indexes a TAB-delimited genome position file in.tab.bgz and creates an index file. |
+| tassel | 3.0 | tassel/3 | None | application | computational biology | While TASSEL has changed considerably since its initial public release in 2001, its primary function continues to be providing tools to investigate the relationship between phenotypes and genotypes1. As indicated by its title – Trait Analysis by aSSociation, Evolution and Linkage – TASSEL has multiple functions, including association study, evaluating evolutionary relationships, analysis of linkage disequilibrium, principal component analysis, cluster analysis, missing data imputation and data visualization. |
+| tassel | 4.0 | tassel/4 | None | application | computational biology | While TASSEL has changed considerably since its initial public release in 2001, its primary function continues to be providing tools to investigate the relationship between phenotypes and genotypes1. As indicated by its title – Trait Analysis by aSSociation, Evolution and Linkage – TASSEL has multiple functions, including association study, evaluating evolutionary relationships, analysis of linkage disequilibrium, principal component analysis, cluster analysis, missing data imputation and data visualization. |
+| tassel | 5.1 | tassel/5.1 | None | application | computational biology | While TASSEL has changed considerably since its initial public release in 2001, its primary function continues to be providing tools to investigate the relationship between phenotypes and genotypes1. As indicated by its title – Trait Analysis by aSSociation, Evolution and Linkage – TASSEL has multiple functions, including association study, evaluating evolutionary relationships, analysis of linkage disequilibrium, principal component analysis, cluster analysis, missing data imputation and data visualization. |
+| taxatortk | 1.3.3 | taxatortk/1.3 | None | application | computational biology | taxator-tk |
+| taxypro | 1.0 | taxypro/1.0 | None | application | mixture modeling for taxonomic analysis of metagenomes | |
+| taxytoolbox | 1.0 | taxytoolbox/1.0 | None | application | mixture modeling for taxonomic analysis of metagenomes | |
+| tensorflow | 0.12.1 | tensorflow/py35/0.12 | None None | application | machine learning | TensorFlow is an open source software library for numerical computation using data flow graphs. |
+| tensorflow | 1.0.0 | tensorflow/py35/1.0 | None None | application | machine learning | TensorFlow is an open source software library for numerical computation using data flow graphs. |
+| tensorflow | 1.3.1 | tensorflow/py35/1.3 | None None None | application | machine learning | TensorFlow is an open source software library for numerical computation using data flow graphs. |
+| tensorflow | 1.4.0 | tensorflow/py36/1.4 | None None None | application | machine learning | TensorFlow is an open source software library for numerical computation using data flow graphs. |
+| tensorflow | 1.5.0 | tensorflow/py35/1.5 | None None None | application | machine learning | TensorFlow is an open source software library for numerical computation using data flow graphs. |
+| tensorflow | 1.7.0 | tensorflow/py35/1.7 | None None None | application | machine learning | TensorFlow is an open source software library for numerical computation using data flow graphs. |
+| tophat | 2.0.14 | tophat/2.0 | None | application | computational biology | TopHat2 is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons. |
+| tophat | 2.1.1 | tophat/2.1 | None | application | computational biology | TopHat2 is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons. |
+| transdecoder | 2.0.1 | transdecoder/2.0 | None | application | computational biology | TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. |
+| transrate | 0.1 | transrate/0.1 | None | application | life sciences | transrate - Quality assessment and comparison of transcriptome assemblies |
+| treemix | 1.12 | treemix/1.12 | None | application | computational biology | TreeMix is a method for inferring the patterns of population splits and mixtures in the history of a set of populations. |
+| trf | 4.07b | trf/4.0 | None | application | computational biology | Tandem Repeats Finder is a program to locate and display tandem repeats in DNA sequences. |
+| trim\_galore | 0.4.0 | trim\_galore/0.4 | None | application | computational biology | Trim sequences |
+| trimmomatic | 0.33 | trimmomatic/0.33 | None | application | computational biology | Trimmomatic: A flexible read trimming tool for Illumina NGS data. |
+| trinity | 2.0 | trinity/2.0 | compiler/gcc/4.8 | application | computational biology | Package for RNA-Seq de novo Assembly |
+| trinity | 2.1 | trinity/2.1 | compiler/gcc/4.8 | application | computational biology | Package for RNA-Seq de novo Assembly |
+| trinity | r2013-02-25 | trinity/r2013-02-25 | None | application | computational biology | Package for RNA-Seq de novo Assembly |
+| trinity | r2013-11-10 | trinity/r2013-11-10 | None | application | computational biology | Package for RNA-Seq de novo Assembly |
+| trinity | r2014-04-13p1 | trinity/r2014-04-13p1 | None | application | computational biology | Package for RNA-Seq de novo Assembly |
+| trinotate | 2.0.2 | trinotate/2.0 | None | application | computational biology | Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. |
+| tvc | 5.2.2 | tvc/5.2 | compiler/gcc/4.9 | application | Bioinformatics | This plugin provides optimized pre-set parameters for many experiment types but is also very customizable. |
+| udunits | 2.1 | udunits/2.1 | compiler/gcc/4.7 compiler/gcc/4.8 compiler/intel/11 compiler/intel/12 compiler/intel/13 compiler/open64/4.5 compiler/pgi/11 compiler/pgi/12 compiler/pgi/13 compiler/pgi/14 compiler/pgi/15 | library | runtime support | |
+| udunits | 2.2 | udunits/2.2 | compiler/intel/11 compiler/intel/12 compiler/intel/13 compiler/intel/15 compiler/pgi/11 compiler/pgi/12 compiler/pgi/13 compiler/pgi/14 compiler/pgi/15 | library | runtime support | |
+| udunits | 2.2.20 | udunits/2.2 | compiler/gcc/4.7 compiler/gcc/4.8 compiler/gcc/4.9 | library | runtime support | |
+| upcr | 2.20 | upcr/2.20 | compiler/gcc/4.9:openmpi/1.8 compiler/gcc/4.9:openmpi/1.8 | application | compiler | |
+| usearch | 7.0 | usearch/7.0 | None | application | computational biology | USEARCH is a unique sequence analysis tool with thousands of users world-wide. USEARCH offers search and clustering algorithms that are often orders of magnitude faster than BLAST. |
+| varscan | 2.3 | varscan/2.3 | None | application | computational biology | VarScan is a platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM, Roche/454, and similar instruments. |
+| vasp | 5.4 | vasp/5.4 | compiler/intel/13:openmpi/1.8 | library | runtime support | |
+| vasp | 5.4.4 | vasp/5.4.4 | compiler/intel/15:openmpi/2.1 | library | runtime support | |
+| vcftools | 0.1 | vcftools/0.1 | None | application | computational biology | VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files. |
+| velvet | 1.2 | velvet/1.2 | None | application | computational biology | Velvet - Sequence assembler for very short reads |
+| viennarna | 2.4.5 | viennarna/2.4 | None | application | computational biology | The ViennaRNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures. |
+| WRF | WRF | WRF/WRF | compiler/pgi/15:openmpi/1.10 None | library | runtime support | |
+| xpclr | 1.0 | xpclr/1.0 | None | application | computational biology | detecting selective sweeps via the differentiation of two populations |
+| xzutils | 5.2 | xzutils/5.2 | None | library | runtime support | |
+| zlib | 1.2 | zlib/1.2 | compiler/gcc/4.7 compiler/gcc/4.8 compiler/gcc/4.9 compiler/intel/11 compiler/intel/12 compiler/intel/13 compiler/intel/15 compiler/open64/4.5 compiler/pgi/11 compiler/pgi/12 compiler/pgi/13 compiler/pgi/14 compiler/pgi/15 None | library | runtime support | |
+
+| Name | Version | Module Name | Prerequisite(s) | Type | Domain | Description |
+|-----------------------|--------------|--------------------------------|-----------------|-------------|---------------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| abayesqr | 1.0 | abayesqr/1.0 | None | application | high-throughput sequencing data | aBayesQR is a viral quasispecies reconstruction algorithm that employs a maximum-likelihood framework to infer individual sequences in a mixture from high-throughput sequencing data. |
+| afni | 18.2.06 | afni/18.2 | None | application | MRI | AFNI is a suite of programs for looking at and analyzing 3D brain images. |
+| afterqc | 0.9.6 | afterqc/0.9 | None | application | package | Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data. AfterQC can simply go through all fastq files in a folder and then output three folders: good, bad and QC folders, which contains good reads, bad reads and the QC results of each fastq file/pair. Currently it supports processing data from HiSeq 2000/2500/3000/4000, Nextseq 500/550, MiniSeq...and other Illumina 1.8 or newer formats. |
+| agfusion | 1.0 | agfusion/1.0 | None | application | Biology | AGFusion is a python package for annotating gene fusions from the human or mouse genomes. |
+| allinea | 18.0 | allinea/18.0 | None | application | Utility | |
+| allinea | 18.2 | allinea/18.2 | None | application | Utility | |
+| allinea | 4.2 | allinea/4.2 | None | application | Utility | |
+| allinea | 5.0 | allinea/5.0 | None | application | Utility | |
+| allinea | 5.1 | allinea/5.1 | None | application | Utility | |
+| allinea | 6.0 | allinea/6.0 | None | application | Utility | |
+| allinea | 6.1 | allinea/6.1 | None | application | Utility | |
+| allinea | 7.0 | allinea/7.0 | None | application | Utility | |
+| ant | 1.10.1 | ant/1.10 | None | library | java | Java build tool |
+| ant | 1.9.9 | ant/1.9 | None | library | java | Java build tool |
+| apkid | 1.0.0 | apkid/1.0 | None | application | Malware | APKiD is Android Application Identifier for Packers, Protectors, Obfuscators and Oddities - PEiD for Android. |
+| aria2 | 1.23.0 | aria2/1.23 | None | application | tool | aria2 is a lightweight multi-protocol & multi-source command-line download utility. |
+| aspera-cli | 3.7.7 | aspera-cli/3.7 | None | application | system | IBM Aspera Command-Line Interface (the Aspera CLI) is a collection of Aspera tools for performing high-speed, secure data transfers from the command line. |
+| augustus | 3.2.3 | augustus/3.2 | None | application | computational biology | AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke and Oliver Keller. It can be used as an ab initio program, which means it bases its prediction purely on the sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources such as EST, MS/MS, protein alignments and synthenic genomic alignments. |
+| augustus | 3.3 | augustus/3.3 | None | application | computational biology | AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke and Oliver Keller. It can be used as an ab initio program, which means it bases its prediction purely on the sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources such as EST, MS/MS, protein alignments and synthenic genomic alignments. |
+| autoconf | 2.69 | autoconf/2.69 | None | application | Utilities | Extensible M4 macros that produce shell scripts to configure software source code packages. |
+| autodock | 4.2.6 | autodock/4.2 | None | application | Chemistry | AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. |
+| awscli | 1.1.120 | awscli/1.11 | None | application | utility | The AWS CLI is an open source tool built on top of the AWS SDK for Python (Boto) that provides commands for interacting with AWS services. |
+| bam-readcount | 0.8 | bam-readcount/0.8 | None | application | computational biology | The purpose of this program is to generate metrics at single nucleotide positions. |
+| bamtools | 2.3.0 | bamtools/2.3 | None | application | computational biology | C++ API & command-line toolkit for working with BAM data |
+| bamtools | 2.4.1 | bamtools/2.4 | None | application | computational biology | C++ API & command-line toolkit for working with BAM data |
+| bbmap | 37.17 | bbmap/37.17 | None | application | computational biology | BBMap is a splice-aware global aligner for DNA and RNA sequencing reads. |
+| bbmap | 38.06 | bbmap/38.06 | None | application | computational biology | BBMap is a splice-aware global aligner for DNA and RNA sequencing reads. |
+| bcftools | 1.3.1 | bcftools/1.3 | None | application | computational biology | BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations. |
+| bcftools | 1.8 | bcftools/1.8 | None | application | computational biology | BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations. |
+| beagle | 4.1\_21Jan17 | beagle/4.1 | None | application | Biology | Beagle is a software package that performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection. |
+| beast | 1.8 | beast/1.8 | None | application | biology | BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC. |
+| beast2 | 2.4 | beast2/2.4 | None | application | biology | BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences. |
+| bedops | 2.4.35 | bedops/2.4 | None | application | computational biology | BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale. |
+| bedtools | 2.24.0 | bedtools/2.24 | None | application | computational biology | A powerful toolset for genome arithmetic |
+| bedtools | 2.27.1 | bedtools/2.27 | None | application | computational biology | A powerful toolset for genome arithmetic |
+| beta | 1.0.7 | beta/1.0 | None | application | computational biology | Binding and Expression Target Analysis (BETA) is a software package that integrates ChIP-seq of transcription factors or chromatin regulators with differential gene expression data to infer direct target genes. |
+| binutils | 2.30 | binutils/2.30 | None | application | Utilities | The GNU Binutils are a collection of binary tools. |
+| bioconductor | 3.4 | bioconductor/3.4 | None | application | computational biology | Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. |
+| bioconductor-ballgown | 2.2.0 | bioconductor-ballgown/2.2 | None | application | computational biology | Tools for statistical analysis of assembled transcriptomes, including flexible differential expression analysis, visualization of transcript structures, and matching of assembled transcripts to annotation. |
+| bioconductor-jmosaics | 1.10 | bioconductor-jmosaics/1.10 | None | application | computational biology | Joint analysis of multiple ChIP-Seq data sets. |
+| biodata | 1.0 | biodata/1.0 | None | application | computational biology | Static data resources for bioinformatics/computational biology. |
+| biom-format | 2.1 | biom-format/2.1 | None | application | computational biology | The BIOM file format (canonically pronounced biome) is designed to be a general-use format for representing biological sample by observation contingency tables. BIOM is a recognized standard for the Earth Microbiome Project and is a Genomics Standards Consortium supported project. |
+| bioperl | 1.6.924 | bioperl/1.6.924 | None | application | computational biology | BioPerl - Perl Modules for Biology |
+| biopython | 1.70 | biopython/py36/1.70 | None None None | library | biological computation | Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. |
+| biopython | 1.71 | biopython/py27/1.71 | None None None | library | biological computation | Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. |
+| blast | 2.6.0 | blast/2.6 | None | application | computational biology | NCBI BLAST+ sequence alignment package. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. |
+| blast | 2.7.1 | blast/2.7 | None | application | computational biology | NCBI BLAST+ sequence alignment package. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. |
+| breakdancer | 1.4 | breakdancer/1.4 | None | application | computational biology | BreakDancer is a Perl/C++ package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads. |
+| breakseq2 | 2.2 | breakseq2/2.2 | None | application | computational biology | BreakSeq2: Ultrafast and accurate nucleotide-resolution analysis of structural variants. |
+| bsmap | 2.90 | bsmap/2.90 | None | application | Mapping | BSMAP is a short reads mapping software for bisulfite sequencing reads. |
+| bx-python | 0.8.1 | bx-python/py27/0.8 | None None None | application | computational biology | Tools for manipulating biological data, particularly multiple sequence alignments |
+| canu | 1.7 | canu/1.7 | None | application | computational biology | Canu is a fork of the Celera Assembler, designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION). |
+| ccat | 3.0 | ccat/3.0 | None | application | computational biology | A software package for the analysis of ChIP-seq data with negative control. |
+| clove | 0.17 | clove/0.17 | None | application | computational biology | CLOVE: Classification of genomic fusions into structural variation events. |
+| clustalw | 2.1 | clustalw/2.1 | None | application | computational biology | ClustalW2 is a multiple sequence alignment tool for the alignment of DNA or protein sequences. |
+| cmake | 2.8.10.2 | cmake/2.8 | None | application | system | CMake is an extensible, open-source system that manages the build process |
+| cmake | 3.10.3 | cmake/3.10 | None | application | system | CMake is an extensible, open-source system that manages the build process |
+| cmake | 3.11.3 | cmake/3.11 | None | application | system | CMake is an extensible, open-source system that manages the build process |
+| cmake | 3.5.0 | cmake/3.5 | None | application | system | CMake is an extensible, open-source system that manages the build process |
+| cmake | 3.7.1 | cmake/3.7 | None | application | system | CMake is an extensible, open-source system that manages the build process |
+| codonw | 1.4.4 | codonw/1.4 | None | application | computational biology | CodonW is a programme designed to simplify the Multivariate analysis (correspondence analysis) of codon and amino acid usage. |
+| connectome-workbench | 1.3.1 | connectome-workbench/1.3 | None | application | neuroimaging | Connectome Workbench is an open source, freely available visualization and discovery tool used to map neuroimaging data, especially data generated by the Human Connectome Project |
+| cutadapt | 1.13 | cutadapt/1.13 | None | application | NGS data | Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. |
+| cutadapt | 1.4 | cutadapt/1.4 | None | application | computational biology | Cutadapt removes adapter sequences from DNA high-throughput sequencing data. |
+| deap | 1.0 | deap/1.0 | None | application | computer science | DEAP is a novel evolutionary computation framework for rapid prototyping and testing of ideas. |
+| deeptools | 2.5.4 | deeptools/2.5 | None | application | computational biology | |
+| detectron/py27 | 2018.09.11 | detectron/py27/2018.09.11 | None | application | object detection | FAIR's research platform for object detection research, implementing popular algorithms like Mask R-CNN and RetinaNet. |
+| eigen | 3.3.3 | eigen/3.3 | None | library | C++ | C++ template library for linear algebra |
+| entrez-direct | 10.0 | entrez-direct/10.0 | None | application | Entrez | Entrez Direct (EDirect) is an advanced method for accessing the NCBI's set of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window. Functions take search terms from command-line arguments. Individual operations are combined to build multi-step queries. Record retrieval and formatting normally complete the process. |
+| eqtlbma | 1.3 | eqtlbma/1.3 | None | application | biology | Package to detect eQTLs jointly in multiple subgroups (e.g. tissues) via Bayesian Model Averaging. |
+| fastqc | 0.11.7 | fastqc/0.11 | None | application | computational biology | fastqc - A Quality Control application for FastQ files |
+| fasttree | 2.1.10 | fasttree/2.1 | None | application | computational biology | FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. |
+| fqtrim | 0.9.7 | fqtrim/0.9 | None | application | computational biology | fqtrim: trimming & filtering of NGS reads. |
+| freebayes | 1.2.0 | freebayes/1.2 | None | application | Biology | Bayesian haplotype-based polymorphism discovery and genotyping |
+| freesurfer | 5.3.0 | freesurfer/5.3 | None | application | computational neuroimaging | An open source software suite for processing and analyzing (human) brain MRI images. |
+| freesurfer | 6.0.0 | freesurfer/6.0 | None | application | computational neuroimaging | An open source software suite for processing and analyzing (human) brain MRI images. |
+| gatk4 | 4.0.4.0 | gatk4/4.0 | None | application | computational biology | GATK4: This toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. |
+| gaussian | 09 RevD | gaussian/09/RevD | None | application | Chemistry | |
+| gaussian | 09 RevE | gaussian/09/RevE | None | application | Chemistry | |
+| gaussian | 16 RevE | gaussian/16/RevA | None | application | Chemistry | |
+| gdcclient | 1.3.0 | gdcclient/1.3 | None | application | genomics | GDC provides a standard client-based mechanism in support of high performance data downloads and submission. |
+| gem | 2.7 | gem/2.7 | None | application | computational biology | GEM: High resolution peak calling and motif discovery for ChIP-seq and ChIP-exo data. |
+| geoparse | 1.0.5 | geoparse/1.0 | None | application | Bioinformatics | Python library to access Gene Expression Omnibus Database (GEO) |
+| ghostscript | 9.20 | ghostscript/9.20 | None | library | runtime support | An interpreter for the PostScript language and for PDF. |
+| ghostscript | 9.22 | ghostscript/9.22 | None | library | runtime support | An interpreter for the PostScript language and for PDF. |
+| git | 2.17.0 | git/2.17 | None | library | tools | distributed version control system |
+| git | 2.7.4 | git/2.7 | None | library | tools | distributed version control system |
+| globus-cli | 1.2.0 | globus-cli/1.2 | None | application | tool | Command line clients provide an interface to Globus services from the shell, and are suited for both interactive use and simple scripting use cases. |
+| glpk | 4.61 | glpk/4.61 | None | application | mathematics | The GLPK (GNU Linear Programming Kit) package is intended for solving large-scale linear programming (LP), mixed integer programming (MIP), and other related problems. It is a set of routines written in ANSI C and organized in the form of a callable library. |
+| gmap | 2015.12.31 | gmap/2015.12.31 | None | application | computational biology | GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and GSNAP: Genomic Short-read Nucleotide Alignment Program. |
+| gmap | 2017.05.08 | gmap/2017.05.08 | None | application | computational biology | GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and GSNAP: Genomic Short-read Nucleotide Alignment Program. |
+| gmap | 2018.03.25 | gmap/2018.03.25 | None | application | computational biology | GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and GSNAP: Genomic Short-read Nucleotide Alignment Program. |
+| gnu-parallel | 20180522 | gnu-parallel/20180522 | None | application | Shell tool | GNU parallel is a shell tool for executing jobs in parallel using one or more computers. |
+| gnuplot | 4.6.0 | gnuplot/4.6 | None | application | unknown | Gnuplot, plotting from command line |
+| gnuplot | 5.2.3 | gnuplot/5.2 | None | application | unknown | Gnuplot, plotting from command line |
+| graphlan | 1.0.0 | graphlan/1.0 | None | application | unknown | GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. It focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation. |
+| graphviz | 2.38.0 | graphviz/2.38 | None | library | unknown | |
+| gtdbtk | 0.1.3 | gtdbtk/0.1 | None | application | computational biology | A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes. |
+| hotspot3d | 0.6.0 | hotspot3d/0.6 | None | application | bioinformatics | This 3D proximity tool can be used to identify mutation hotspots from linear protein sequence and correlate the hotspots with known or potentially interacting domains, mutations, or drugs. Mutation-mutation and mutation-drug clusters can also be identified and viewed. |
+| htseq | 0.5.4p5 | htseq/0.5.4p5 | None | application | computational biology | HTSeq - Analysing high-throughput sequencing data with Python |
+| htseq | 0.6.1p1 | htseq/0.6.1p1 | None | application | computational biology | HTSeq - Analysing high-throughput sequencing data with Python |
+| htseq | 0.9.1 | htseq/0.9 | None | application | computational biology | HTSeq - Analysing high-throughput sequencing data with Python |
+| htslib | 1.7 | htslib/1.7 | None | application | computational biology | HTSlib is an implementation of a unified C library for accessing common file formats. |
+| htstream | e919d21 | htstream/e919d21 | None | application | Bioinformatics | A toolset for high throughput sequence analysis using a streaming approach facilitated by Linux pipes. |
+| imagemagick | 7.0.8\_10 | imagemagick/7.0 | None | application | bitmap | Software suite to create, edit, compose, or convert bitmap images. |
+| impute2 | 2.3.2 | impute2/2.3 | None | application | computational biology | IMPUTE2 is a computer program for phasing observed genotypes and imputing missing genotypes. |
+| iqtree | 1.6.7 | iqtree/1.6 | None | application | computational biology | IQ-TREE creates phylogenetic trees under maximum likelihood with emphasis on speed and accuracy. |
+| jamm | 1.0.7r2 | jamm/1.0.7r2 | None | application | computational biology | JAMM is a peak finder for NGS datasets (ChIP-Seq, ATAC-Seq, DNase-Seq..etc.) that can integrate replicates and assign peak boundaries accurately. |
+| java | 1.6 | java/1.6 | None | application | system | Java JDK. |
+| java | 1.7 | java/1.7 | None | application | system | Java JDK. |
+| java | 1.8 | java/1.8 | None | application | system | Java JDK. |
+| julia | 1.0 | julia/1.0 | None | application | Language | A high-performance dynamic programming language for data science |
+| jvarkit-msa2vcf | 1.0 | jvarkit-msa2vcf/1.0 | None | application | computational biology | Getting a VCF file from a CLUSTAW or a FASTA alignment. |
+| jvarkit-sam2tsv | 1.0 | jvarkit-sam2tsv/1.0 | None | application | computational biology | Prints the SAM alignments as a TAB delimited file. |
+| kalign | 2.0 | kalign/2.0 | None | application | computational biology | Kalign is a fast and accurate multiple sequence alignment algorithm designed to align large numbers of protein sequences. |
+| ksnp | 3.1 | ksnp/3.1 | None | application | computational biology | kSNP identifies the pan-genome SNPs in a set of genome sequences, and estimates phylogenetic trees based upon those SNPs. |
+| lftp | 4.8.3 | lftp/4.8 | None | application | system | LFTP is a sophisticated file transfer program supporting a number of network protocols (ftp, http, sftp, fish, torrent). |
+| lynx | 2.8.8 | lynx/2.8 | None | application | tool | Lynx is a text browser for the World Wide Web. |
+| macs2 | 2.1.1 | macs2/2.1 | None | application | computational biology | MACS -- Model-based Analysis of ChIP-Seq |
+| maker | 2.31.9 | maker/2 | None | application | computational biology | MAKER is a genome annotation pipeline for prokaryotic and smaller eukaryotic organisms. |
+| mapsplice | 2.2.0 | mapsplice/2.2 | None | application | computational biology | MapSplice is a software for mapping RNA-seq data to reference genome for splice junction discovery that depends only on reference genome, and not on any further annotations. |
+| mathematica | 10.0 | mathematica/10.0 | None | application | unknown | |
+| mathematica | 10.4 | mathematica/10.4 | None | application | unknown | |
+| mathematica | 11.0 | mathematica/11.0 | None | application | unknown | |
+| mathematica | 9.0 | mathematica/9.0 | None | application | unknown | |
+| matlab | r2012b | matlab/r2012b | None | application | unknown | |
+| matlab | r2013b | matlab/r2013b | None | application | unknown | |
+| matlab | r2014b | matlab/r2014b | None | application | unknown | |
+| matlab | r2015b | matlab/r2015b | None | application | unknown | |
+| matlab | r2016a | matlab/r2016a | None | application | unknown | |
+| matlab | r2016b | matlab/r2016b | None | application | unknown | |
+| matlab | r2017a | matlab/r2017a | None | application | unknown | |
+| matlab | r2017b | matlab/r2017b | None | application | unknown | |
+| matlab | r2018a | matlab/r2018a | None | application | unknown | |
+| mbuffer | 20171011 | mbuffer/20171011 | None | application | buffer | Mbuffer is a tool for buffering data streams with a large set of unique features. |
+| mcl | 14.137 | mcl/14.137 | None | application | computational biology | MCL |
+| megahit | 1.1 | megahit/1.1 | None | application | computational biology | MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. |
+| metasv | 0.5.4 | metasv/0.5 | None | application | computational biology | An accurate and integrative structural-variant caller for next generation sequencing. |
+| mlpack | 3.0.3 | mlpack/3.0 | None | library | Machine Learning | mlpack a fast, flexible machine learning library |
+| multiqc | 1.6 | multiqc/py27/1.6 | None None None | application | computational biology | MultiQC is a tool to create a single report with interactive plots for multiple bioinformatics analyses across many samples. |
+| mummer4 | 4.0.0beta2 | mummer4/4.0 | None | application | Bioinformatics | MUMmer is a system for rapidly aligning entire genomes |
+| mxnet | 0.9.3a | mxnet/0.9.3 | None | application | AI | MXNet is an open-source deep learning framework that allows you to define, train, and deploy deep neural networks on a wide array of devices, from cloud infrastructure to mobile devices. |
+| ncbi-download | 0.2.6 | ncbi-download/0.2 | None | application | computational biology | Python scriopt for downloading bacterial and fungal genomes from NCBI. |
+| neper | 3.3.0 | neper/3.3 | None | application | Applications | Neper is a software package for polycrystal generation and meshing. |
+| octave | 4.2 | octave/4.2 | None | application | engineering | GNU Octave is a high-level language, primarily intended for numerical computations. It provides a convenient command line interface for solving linear and nonlinear problems numerically, and for performing other numerical experiments using a language that is mostly compatible with Matlab. |
+| opencv | 3.4.1 | opencv/py27/3.4 | None None | library | unknown | OpenCV is a computer vision and machine learning software library. |
+| orthofinder | 1.1.8 | orthofinder/1.1 | None | application | computational biology | OrthoFinder is a fast, accurate and comprehensive analysis tool for comparative genomics. |
+| orthofinder | 2.2.6 | orthofinder/2.2 | None | application | computational biology | OrthoFinder is a fast, accurate and comprehensive analysis tool for comparative genomics. |
+| paml | 4.9 | paml/4.9 | None | application | Sequencing | Phylogenetic Analysis by Maximum Likelihood (PAML) |
+| pandaseq | 2.11 | pandaseq/2.11 | None | application | bioinformatics | PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence. |
+| peakranger | 1.18 | peakranger/1.18 | None | application | computational biology | PeakRanger is a multi-purporse software suite for analyzing next-generation sequencing (NGS) data. |
+| peakzilla | 1.0 | peakzilla/1.0 | None | application | computational biology | Peakzilla identifies sites of enrichment and transcription factor binding sites from transcription factor ChIP-seq and ChIP-exo experiments at hight accuracy and resolution. |
+| pepr | 1.1.18 | pepr/1.1 | None | application | computational biology | Peak-calling and Prioritization pipeline for replicated ChIP-Seq data. |
+| perl | 5.22 | perl/5.22 | None | application | perl | The Perl Programming Language |
+| phylosnp | 1.0 | phylosnp/1.0 | None | application | computational biology | PhyloSNP is designed to take SNP data files (.csv and .vcf) and generate phylogenetic trees from the provided data. |
+| picard | 2.18.4 | picard/2.18 | None | application | computational biology | A set of Java command line tools for manipulating high-throughput sequencing data (HTS) data and formats. |
+| picard | 2.9.0 | picard/2.9 | None | application | computational biology | A set of Java command line tools for manipulating high-throughput sequencing data (HTS) data and formats. |
+| pindel | 0.2.5b9 | pindel/0.2 | None | application | computational biology | |
+| pirs | 2.0.2 | pirs/2.0 | None | application | computational biology | |
+| plink | 1.90b4 | plink/1.90 | None | application | computational biology | PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. |
+| plinkseq | 0.10 | plinkseq/0.10 | None | application | computational biology | PLINK/SEQ is an open-source C/C++ library for working with human genetic variation data. |
+| pomoxis | 0.1.7 | pomoxis/0.1 | None | application | computational biology | Pomoxis comprises APIs and command line tools for interacting and analysing Oxford Nanopore Technologies’ data in real time. |
+| prokka | 1.12 | prokka/1.12 | None | application | bioinformatics | Prokka is a software tool for the rapid annotation of prokaryotic genomes. |
+| pullseq | 1.0 | pullseq/1.0 | None | application | computational biology | pullseq - Software to extract sequence from a fasta or fastq. Also filter sequences by a minimum length or maximum length. |
+| pyclone | 0.13 | pyclone/0.13 | None | application | computational biology | PyClone is statistical model and software tool designed to infer the prevalence of point mutations in heterogeneous cancer samples. |
+| pyfasta | 0.5 | pyfasta/0.5 | None | application | computational biology | Pyfasta - fast, memory-efficient, pythonic (and command-line) access to fasta sequence files. |
+| pygenometracks | 2.0 | pygenometracks/2.0 | None | application | bioinformatics | Standalone program and library to plot beautiful genome browser tracks. |
+| pymongo | 3.0.3 | pymongo/3.0 | None | application | Utility | PyMongo is a Python distribution containing tools for working with MongoDB, and is the recommended way to work with MongoDB from Python. |
+| pymongo | 3.3.0 | pymongo/3.3 | None | application | Utility | PyMongo is a Python distribution containing tools for working with MongoDB, and is the recommended way to work with MongoDB from Python. |
+| python | 2.7 | python/2.7 | None | application | system | |
+| python | 3.4 | python/3.4 | None | application | system | |
+| python | 3.5 | python/3.5 | None | application | system | |
+| python | 3.6 | python/3.6 | None | application | system | |
+| python | 3.7 | python/3.7 | None | application | system | |
+| pytorch | 0.4.0 | pytorch/py36/0.4 | None None None | application | deep learning | PyTorch is an optimized tensor library for deep learning using GPUs and CPUs. |
+| qiime2 | 2018.4 | qiime2/2018.4 | None | application | computational biology | QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency. |
+| quasr | 6.09 | quasr/6.09 | None | application | computational biology | QUASR is lightweight pipeline for processing and analysis of high-throughput sequencing data. |
+| quast | 4.4 | quast/4.4 | None | application | computational biology | QUAST evaluates genome assemblies by computing various metrics. |
+| quast | 4.5 | quast/4.5 | None | application | computational biology | QUAST evaluates genome assemblies by computing various metrics. |
+| R | 3.4.4 | R/3.4 | None | application | mathematics | Microsoft R Open is the enhanced distribution of R from Microsoft Corporation. |
+| R | 3.5.1 | R/3.5 | None | application | mathematics | Microsoft R Open is the enhanced distribution of R from Microsoft Corporation. |
+| rarefactionanalyzer | 2018.09.06 | rarefactionanalyzer/2018.09.06 | None | application | computational biology | Rarefaction analyzer is a simple program that can be used to perform rarefaction analysis. |
+| rclone | 1.44 | rclone/1.44 | None | application | Storage | Rclone - rsync for cloud storage. |
+| red | 2015.05.22 | red/2015.05.22 | None | application | Genomics | Red (RepeatsDetector): an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale. |
+| regtools | 0.5.0 | regtools/0.5 | None | application | bioinformatics | Tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context. |
+| repenrich | 1.2 | repenrich/1.2 | None | application | computational biology | RepEnrich is a method to estimate repetitive element enrichment using high-throughput sequencing data. |
+| resistomeanalyzer | 2018.09.06 | resistomeanalyzer/2018.09.06 | None | application | computational biology | Resistome Analyzer is a simple tool for analyzing the resistome of large metagenomic datasets. |
+| revtrans | 1.4 | revtrans/1.4 | None | application | computational biology | RevTrans - performs a reverse translation of a peptide alignment. |
+| r-genometricorr | 1.1.17 | r-genometricorr/1.1 | None | application | Genomics | Genometric Correlation (GenometriCorr) is an R package for spatial correlation of genome-wide interval datasets. |
+| r-ggfortify | 0.4.1 | r-ggfortify/0.4 | None | application | r | ggfortify is a package of unified plotting tools for statistics commonly used, such as GLM, time series, PCA families, clustering and survival analysis. |
+| rgt | 0.11.4 | rgt/0.11 | None | application | computational biology | Toolkit to perform regulatory genomics data analysis |
+| r-markdown | 0.8 | r-markdown/0.8 | None | application | R | Markdown is a plain-text formatting syntax that can be converted to XHTML or other formats. |
+| rnastructure | 6.1 | rnastructure/6.1 | None | application | Bioinformatics | RNAstructure is a complete package for RNA and DNA secondary structure prediction and analysis. It includes algorithms for secondary structure prediction, including facility to predict base pairing probabilities. It also can be used to predict bimolecular structures and can predict the equilibrium binding affinity of an oligonucleotide to a structured RNA target. This is useful for siRNA design. It can also predict secondary structures common to two, unaligned sequences, which is much more accurate than single sequence secondary structure prediction. Finally, RNAstructure can take a number of different types of experiment mapping data to constrain or restrain structure prediction. These include chemical mapping, enzymatic mapping, NMR, and SHAPE data. |
+| r-regresshaplo | 1.0 | r-regresshaplo/1.0 | None | application | biology | This package reconstructs haplotypes from a BAM file using a penalized regression approach. |
+| r-scimpute | 0.0.6 | r-scimpute/0.0.6 | None | application | biology | scImpute is accurate and robust imputation of single-cell RNA sequencing data. |
+| rsem | 1.3 | rsem/1.3 | None | application | computational biology | RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. |
+| r-seqminer | 6.0 | r-seqminer/6.0 | None | application | biology | SEQMINER is for sequencing variant annotation, data integration and query in R. |
+| r-vcfr | 1.5.0 | r-vcfr/1.5 | None | application | biology | A package to manipulate and visualize VCF data in R. |
+| salmon | 0.6.0 | salmon/0.6 | None | application | computational biology | Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments. |
+| salmon | 0.8.2 | salmon/0.8 | None | application | computational biology | Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments. |
+| salmon | 0.9.1 | salmon/0.9 | None | application | computational biology | Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments. |
+| samtools | 1.5 | samtools/1.5 | None | application | computational biology | SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. |
+| samtools | 1.6 | samtools/1.6 | None | application | computational biology | SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. |
+| samtools | 1.9 | samtools/1.9 | None | application | computational biology | Tools for dealing with SAM, BAM and CRAM files |
+| sas | 9.3 | sas/9.3 | None | application | Applications | SAS is a software suite developed by SAS Institute for advanced analytics, business intelligence, data management, and predictive analytics. |
+| sas | 9.4 | sas/9.4 | None | application | Applications | SAS is a software suite developed by SAS Institute for advanced analytics, business intelligence, data management, and predictive analytics. |
+| scons | 2.5 | scons/2.5 | None | application | utility | SCons: A software construction tool. |
+| scons | 3.0 | scons/3.0 | None | application | utility | SCons: A software construction tool. |
+| seedme | 1.2 | seedme/1.2 | None | application | Utility | Client program for SeedMe.org. |
+| selecton | 2.4 | selecton/2.4 | None | application | Bioinformatics | Selecton 2007: advanced models for detecting positive and purifying selection using a Bayesian inference approach. |
+| seqtk | 1.2 | seqtk/1.2 | None | application | computational biology | Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. |
+| seqyclean | 1.10.07 | seqyclean/1.10 | None | application | Bioinformatics | Main purpose of this software is to pre-process NGS data in order to prepare for downstream analysis. |
+| shapeit | 2.0 | shapeit/2.0 | None | application | computational biology | SHAPEIT is a fast and accurate method for estimation of haplotypes (aka phasing) from genotype or sequencing data. |
+| sift4g | 2.0.0 | sift4g/2.0 | None | application | computational biology | SIFT 4G is a faster version of SIFT that enables us to scale up and provide SIFT predictions for more organisms. |
+| singularity | 2.2 | singularity/2.2 | None | application | system | Application containers enabling mobility of compute. |
+| singularity | 2.3 | singularity/2.3 | None | application | system | Application containers enabling mobility of compute. |
+| singularity | 2.4 | singularity/2.4 | None | application | system | Application containers enabling mobility of compute. |
+| singularity | 2.6 | singularity/2.6 | None | application | system | Application containers enabling mobility of compute. |
+| snpeff | 4.3 | snpeff/4.3 | None | application | computational biology | Genetic variant annotation and effect prediction toolbox. |
+| snpfinder | 1.0.0 | snpfinder/1.0 | None | application | computational biology | SNPFinder is a simple alignment-based haplotype variant caller that can be used with metagenomic sequence data. |
+| snp-pipeline | 0.7 | snp-pipeline/0.7 | None | application | computational biology | SNP Pipeline is a pipeline for the production of SNP matrices from sequence data used in the phylogenetic analysis of pathogenic organisms sequenced from samples of interest to food safety. |
+| snp-pipeline | 1.0 | snp-pipeline/1.0 | None | application | unknown | |
+| snp-sites | 2.3.3 | snp-sites/2.3 | None | application | computational biology | SNP-sites rapidly extracts SNPs from a multi-FASTA alignment. |
+| soapdenovo-trans | 1.04 | soapdenovo-trans/1.04 | None | application | computational biology | SOAPdenovo-Trans is a de novo transcriptome assembler basing on the SOAPdenovo framework, adapt to alternative splicing and different expression level among transcripts. |
+| sonnet | 1.13 | sonnet/py27/1.13 | None None None | application | machine learning | Sonnet is a library built on top of TensorFlow for building complex neural networks. |
+| sonnet | 1.19 | sonnet/py27/1.19 | None None None | application | machine learning | Sonnet is a library built on top of TensorFlow for building complex neural networks. |
+| sonnet | 1.23 | sonnet/py35/1.23 | None None None | application | machine learning | Sonnet is a library built on top of TensorFlow for building complex neural networks. |
+| spades | 3.10.1 | spades/3.10 | None | application | computational biology | SPAdes - St. Petersburg genome assembler - is intended for both standard isolates and single-cell MDA bacteria assemblies. |
+| spades | 3.11.1 | spades/3.11 | None | application | computational biology | SPAdes - St. Petersburg genome assembler - is intended for both standard isolates and single-cell MDA bacteria assemblies. |
+| spades | 3.12.0 | spades/3.12 | None | application | computational biology | SPAdes - St. Petersburg genome assembler - is intended for both standard isolates and single-cell MDA bacteria assemblies. |
+| spades | 3.8.1 | spades/3.8 | None | application | computational biology | SPAdes - St. Petersburg genome assembler - is intended for both standard isolates and single-cell MDA bacteria assemblies. |
+| ssake | 4.0 | ssake/4.0 | None | application | genomics | SSAKE is a genomics application for de novo assembly of millions of very short DNA sequences. |
+| stereogene | 2.20 | stereogene/2.20 | None | application | sequencing | StereoGene: Rapid Estimation of Genomewide Correlation of Continuous or Interval Feature Data |
+| targetfinder | 1.7 | targetfinder/1.7 | None | application | computational biology | Plant small RNA target prediction tool. |
+| tassel | 5.2.40 | tassel/5.2 | None | application | computational biology | TASSEL is a software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium. |
+| tax2tree | 1.0 | tax2tree/1.0 | None | application | computational biology | tax2tree - Tools for decorating taxonomy information on to a phylogenetic tree. |
+| tensorflow | 1.11.0 | tensorflow/py27/1.11 | None None | application | machine learning | TensorFlow is an open source software library for numerical computation using data flow graphs. |
+| theano | 0.9.0 | theano/py27/0.9 | None None None | application | mathematics | Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently. |
+| theano | 1.0.2 | theano/py36/1.0 | None None None | application | mathematics | Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently. |
+| transdecoder | 3.0.1 | transdecoder/3.0 | None | application | computational biology | TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. |
+| treemix | 1.13 | treemix/1.13 | None | application | computational biology | TreeMix is a method for inferring the patterns of population splits and mixtures in the history of a set of populations. |
+| trimmomatic | 0.36 | trimmomatic/0.36 | None | application | computational biology | Trimmomatic: A flexible read trimming tool for Illumina NGS data. |
+| trimmomatic | 0.38 | trimmomatic/0.38 | None | application | computational biology | A flexible read trimming tool for Illumina NGS data |
+| trinity | 2.4.0 | trinity/2.4 | None | application | computational biology | Trinity assembles transcript sequences from Illumina RNA-Seq data. |
+| trinity | 2.6.6 | trinity/2.6 | None | application | computational biology | Trinity RNA-Seq de novo transcriptome assembly |
+| ucsc-liftover | 366 | ucsc-liftover/366 | None | application | computational biology | The Batch Coordinate Conversion (liftOver) utility converts genome coordinates and genome annotation files between assemblies. |
+| viennarna | 2.3.3 | viennarna/2.3 | None | application | computational biology | The ViennaRNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures. |
+| xcrysden | 1.5.60 | xcrysden/1.5 | None | application | physics | XCrySDen is a crystalline and molecular structure visualisation program aiming at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated. |
+| zerone | 1.0 | zerone/1.0 | None | application | computational biology | Zerone discretizes several ChIP-seq replicates simultaneously and resolves conflicts between them. After the job is done, Zerone checks the results and tells you whether it passes the quality control. |
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8192301/35324470.xml) (text/xml)
+
+Document generated by Confluence on Oct 24, 2018 14:48
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/bioinformatics_tools/_index.md b/content/guides/running_applications/bioinformatics_tools/_index.md
new file mode 100644
index 00000000..b5319f96
--- /dev/null
+++ b/content/guides/running_applications/bioinformatics_tools/_index.md
@@ -0,0 +1,17 @@
++++
+title = "Bioinformatics Tools"
++++
+
+<span style="color: rgb(0,0,0);">The following is a categorized list of
+bioinformatics tools available on HCC. Each page contains summary of the
+tool, information about the HCC resources that have the specific
+tool, links to user documentation, as well as example SLURM submit
+scripts. More detailed information about submitting SLURM jobs and
+checking job status on HCC can be
+found [here](Submitting-Jobs_332222.html).</span>
+
+<span style="color: rgb(0,0,0);"> </span>
+
+Document generated by Confluence on Oct 24, 2018 14:48
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/bioinformatics_tools/alignment_tools/_index.md b/content/guides/running_applications/bioinformatics_tools/alignment_tools/_index.md
new file mode 100644
index 00000000..7d754341
--- /dev/null
+++ b/content/guides/running_applications/bioinformatics_tools/alignment_tools/_index.md
@@ -0,0 +1,20 @@
++++
+title = "Alignment Tools"
++++
+
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Running Applications](Running-Applications_7471153.html)
+5. [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
+
+<span id="title-text"> HCC-DOCS : Alignment Tools </span>
+=========================================================
+
+Created by <span class="author"> Adam Caprez</span> on Sep 04, 2014
+
+
+
+Document generated by Confluence on Oct 24, 2018 14:48
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/_index.md b/content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/_index.md
new file mode 100644
index 00000000..b2d9ece0
--- /dev/null
+++ b/content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/_index.md
@@ -0,0 +1,1177 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Running Applications](Running-Applications_7471153.html)
+5. [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
+6. [Alignment Tools](Alignment-Tools_8193288.html)
+
+<span id="title-text"> HCC-DOCS : BLAST </span>
+===============================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified by
+<span class="editor"> Natasha Pavlovikj</span> on Sep 07, 2018
+
+| Name | Version | Resource |
+|-------|---------|----------|
+| blast | 2.2.30 | Tusker |
+| blast | 2.4.0 | Tusker |
+
+
+
+| Name | Version | Resource |
+|-------|---------|----------|
+| blast | 2.6.0 | Tusker |
+| blast | 2.7.1 | Tusker |
+
+
+
+| | | |
+|-------|--------|-------|
+| blast | 2.2.29 | Crane |
+| blast | 2.2.30 | Crane |
+| blast | 2.4.0 | Crane |
+
+
+
+| | | |
+|-------|-------|-------|
+| blast | 2.6.0 | Crane |
+| blast | 2.7.1 | Crane |
+
+
+
+BLAST
+(<a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi" class="external-link">http://blast.ncbi.nlm.nih.gov/Blast.cgi</a>)
+is a local alignment tool that finds similarity between sequences. This
+tool compares nucleotide or protein sequences to sequence databases, and
+calculates significance of matches. Sometimes these input sequences are
+large and using the command-line BLAST is required.
+
+The following pages, [Create Local BLAST
+Database](Create-Local-BLAST-Database_8193290.html) and [Running BLAST
+Alignment](Running-BLAST-Alignment_8193291.html) describe how to run
+some of the most common BLAST executables as a single job under the
+SLURM scheduler on HCC.
+
+
+
+**Useful Information**
+
+In order to test the BLAST (blast/2.2) performance on Tusker, we aligned
+three nucleotide query datasets, **small.fasta**, **medium.fasta** and
+**large.fasta**, against the non-redundant nucleotide **nt.fasta**
+database from NCBI. Some statistics about the query datasets and the
+time and memory resources required for the alignment are shown on the
+table below:
+
+| | **total \# of sequences** | **total \# of bases** | **total size in MB** | **required time** | **required memory** | \# of used CPUs |
+|------------------|---------------------------|-----------------------|----------------------|-------------------|---------------------|-----------------|
+| **small.fasta** | 41,715 | 35,581,740 | 37.627 MB | \~ 2 hours | \~ 23 GB | 8 |
+| **medium.fasta** | 110,478 | 147,543,113 | 149 MB | \~ 4 hours | \~ 24 GB | 8 |
+| **large.fasta** | 592,593 | 827,629,204 | 836 MB | \~ 15 hours | \~ 47 GB | 8 |
+
+
+
+
+
+
+
+
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_blast\_version.xsl](attachments/8193289/8127538.xsl)
+(application/octet-stream)
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+[hcc\_modules.xml](attachments/8193289/35325892.xml) (text/xml)
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193289/35326672.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193289/35326314.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193289/35326408.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193289/35326436.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193289/35326504.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193289/35326554.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193289/35326593.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193289/35326644.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193289/35326666.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193289/35326824.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193289/16521358.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193289/16521359.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193289/35326901.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193289/35326936.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193289/35326955.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193289/35327037.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193289/35325378.xml) (text/xml)
+
+Document generated by Confluence on Oct 24, 2018 14:48
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/create_local_blast_database.md b/content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/create_local_blast_database.md
new file mode 100644
index 00000000..71d6bf4a
--- /dev/null
+++ b/content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/create_local_blast_database.md
@@ -0,0 +1,486 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Running Applications](Running-Applications_7471153.html)
+5. [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
+6. [Alignment Tools](Alignment-Tools_8193288.html)
+7. [BLAST](BLAST_8193289.html)
+
+<span id="title-text"> HCC-DOCS : Create Local BLAST Database </span>
+=====================================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified by
+<span class="editor"> Natasha Pavlovikj</span> on Sep 07, 2018
+
+The basic way to create a local BLAST database is to use the
+**makeblastdb** command:
+
+**General Makeblastdb Usage**
+
+``` syntaxhighlighter-pre
+makeblastdb -in input_reads.fasta -dbtype [nucl|prot] -out input_reads_db
+```
+
+where **input\_reads.fasta** is the input file containing all sequences
+that need to be made into a database, and **dbtype** can be either
+*nucl* or *prot* depending on the type of the input file.
+
+Simple example of how **makeblastdb** can be run on Tusker using SLURM
+script and nucleotide database is shown below:
+
+**blast\_db.submit**
+
+\#!/bin/sh
+\#SBATCH --job-name=Blast\_DB
+\#SBATCH --nodes=1
+\#SBATCH --ntasks-per-node=1
+\#SBATCH --time=168:00:00
+\#SBATCH --mem=50gb
+\#SBATCH --output=BlastDB.%J.out
+\#SBATCH --error=BlastDB.%J.err
+
+
+
+| |
+|-----------------------|
+| module load blast/2.7 |
+
+makeblastdb -in input\_reads.fasta -dbtype nucl -out input\_reads\_db
+
+More parameters used with **makeblastdb** can be seen by typing:
+
+**Additional Makeblastdb Options**
+
+``` syntaxhighlighter-pre
+[<username>@login.tusker ~]$ makeblastdb -help
+```
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[cb\_blast\_module.xsl](attachments/8193290/8127542.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193290/8127543.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193290/30446033.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193290/30446179.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193290/30446285.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193290/30446392.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193290/30446584.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193290/30446643.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193290/30446820.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193290/30446922.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193290/30447084.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193290/30447146.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193290/30447255.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193290/30447479.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193290/30447583.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193290/30447656.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193290/30447756.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193290/30447991.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193290/30448091.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193290/30448297.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193290/30448440.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193290/30448667.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193290/30448770.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193290/30448877.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193290/30448985.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193290/33685606.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193290/33685717.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193290/33685829.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193290/33685934.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193290/33686071.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193290/33686175.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193290/33686314.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193290/33687850.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193290/33688458.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193290/33689783.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193290/33690003.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193290/35324043.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193290/35324153.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193290/35324623.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193290/35324913.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193290/35325645.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193290/35325456.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193290/35325482.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193290/35325501.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193290/35325534.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193290/35325871.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193290/35325758.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193290/35326745.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193290/35325890.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193290/35325918.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193290/35325937.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193290/35325968.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193290/35326026.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193290/35326097.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193290/35326210.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193290/35326312.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193290/35326406.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193290/35326434.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193290/35326502.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193290/35326552.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193290/35326591.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193290/35326642.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193290/35326664.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193290/35326822.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193290/17044365.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193290/35326899.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193290/35326934.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193290/35326953.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193290/35327035.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193290/35325376.xml) (text/xml)
+
+Document generated by Confluence on Oct 24, 2018 14:48
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/running_blast_alignment.md b/content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/running_blast_alignment.md
new file mode 100644
index 00000000..8b00ea73
--- /dev/null
+++ b/content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/running_blast_alignment.md
@@ -0,0 +1,718 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Running Applications](Running-Applications_7471153.html)
+5. [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
+6. [Alignment Tools](Alignment-Tools_8193288.html)
+7. [BLAST](BLAST_8193289.html)
+
+<span id="title-text"> HCC-DOCS : Running BLAST Alignment </span>
+=================================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified by
+<span class="editor"> Natasha Pavlovikj</span> on Sep 07, 2018
+
+Basic BLAST has the following commands:
+
+- **blastn**: search nucleotide database using a nucleotide query
+- **blastp**: search protein database using a protein query
+- **blastx**: search protein database using a translated nucleotide
+ query
+- **tblastn**: search translated nucleotide database using a protein
+ query
+- **tblastx**: search translated nucleotide database using a
+ translated nucleotide query
+
+The basic usage of **blastn** is:
+
+**General BLASTN Usage**
+
+``` syntaxhighlighter-pre
+blastn -query input_reads.fasta -db input_reads_db -out blastn_output.alignments [options]
+```
+
+where **input\_reads.fasta** is an input file of sequence data in fasta
+format, **input\_reads\_db** is the generated BLAST database, and
+**blastn\_output.alignments** is the output file where the alignments
+are stored. Additional parameters can be found in the BLAST
+manual: <a href="http://www.ncbi.nlm.nih.gov/books/NBK1763/" class="external-link">http://www.ncbi.nlm.nih.gov/books/NBK1763/</a>,
+or by typing:
+
+**Additional BLASTN Options**
+
+``` syntaxhighlighter-pre
+[<username>@login.tusker ~]$ blastn -help
+```
+
+These BLAST alignment commands are multi-threaded, and therefore using
+the BLAST option **-num\_threads <number\_of\_CPUs>** is
+recommended.
+
+
+
+HCC hosts multiple BLAST databases and indices on both Tusker and Crane.
+In order to use these resources, the "biodata" module needs to be loaded
+first, <https://hcc-docs.unl.edu/x/L4Hn>. The **$BLAST** variable
+contains** **the following currently available databases:
+
+- **16SMicrobial**
+- **env\_nt**
+- **est**
+- **est\_human**
+- **est\_mouse**
+- **est\_others**
+- **gss**
+- **human\_genomic**
+- **human\_genomic\_transcript**
+- **mouse\_genomic\_transcript**
+- **nr**
+- **nt**
+- **other\_genomic**
+- **refseq\_genomic**
+- **refseq\_rna**
+- **sts**
+- **swissprot**
+- **tsa\_nr**
+- **tsa\_nt**
+
+If you want to create and use a BLAST database that is not mentioned
+above, check [Create Local BLAST
+Database](Create-Local-BLAST-Database_8193290.html).
+
+
+
+Basic SLURM example of nucleotide blast run against the
+non-redundant **nt** BLAST database downloaded on HCC with 8 CPUs is
+provided below.
+When running BLAST alignment, it is recommended to first copy the query
+and database files to the *scratch/* directory on the worker node.
+Moreover, the blast output is also saved in this directory
+(*/scratch/blastn\_output.alignments*). After BLAST finishes, the output
+file is copied from the worker node to your current work directory on
+the login node.
+
+**Please note that the worker nodes can not write to the */home*
+directories and therefore you need to run your job from your */work*
+directory.**
+
+**blastn\_alignment.submit**
+
+\#!/bin/sh
+\#SBATCH --job-name=BlastN
+\#SBATCH --nodes=1
+\#SBATCH --ntasks-per-node=8
+\#SBATCH --time=168:00:00
+\#SBATCH --mem=20gb
+\#SBATCH --output=BlastN.%J.out
+\#SBATCH --error=BlastN.%J.err
+
+
+module load biodata/1.0
+
+module load blast/2.7
+
+cd $WORK/<project\_folder>
+
+cp $BLAST/nt.\* /scratch/
+cp <span style="line-height: 1.4285715;">input\_reads.fasta</span>
+/scratch/
+
+blastn -query /scratch/input\_reads.fasta -db /scratch/nt -out
+/scratch/blastn\_output.alignments -num\_threads
+$SLURM\_NTASKS\_PER\_NODE
+
+cp /scratch/blastn\_output.alignments $WORK/<project\_folder>
+
+
+
+One important BLAST parameter is the **e-value threshold** that changes
+the number of hits returned by showing only those with value lower than
+the given. To show the hits with **e-value** lower than 1e-10, modify
+the given script as follows:
+
+**BLASTN with E-value Option**
+
+``` syntaxhighlighter-pre
+blastn -query input_reads.fasta -db input_reads_db -out blastn_output.alignments -num_threads $SLURM_NTASKS_PER_NODE -evalue 1e-10
+```
+
+The default BLAST output is in pairwise format. However, BLAST’s
+parameter **-outfmt** supports output in different formats that are
+easier for parsing
+(<a href="https://www.ncbi.nlm.nih.gov/books/NBK279675/" class="external-link">https://www.ncbi.nlm.nih.gov/books/NBK279675/</a>).
+
+
+
+Basic SLURM example of protein blast run against the
+non-redundant **nr **BLAST database downloaded on HCC with tabular
+output format and 8 CPUs is shown below.
+The query and database files are copied to the *scratch/* directory. The
+blast output is also saved in this directory
+(*/scratch/blastx\_output.alignments*). After BLAST finishes, the output
+file is copied from the worker node to your current work directory on
+the login node.
+
+**Please note that the worker nodes can not write to
+the */home* directories and therefore you need to run your job from
+the */work* directory.**
+
+**blastx\_alignment.submit**
+
+\#!/bin/sh
+\#SBATCH --job-name=BlastX
+\#SBATCH --nodes=1
+\#SBATCH --ntasks-per-node=8
+\#SBATCH --time=168:00:00
+\#SBATCH --mem=20gb
+\#SBATCH --output=BlastX.%J.out
+\#SBATCH --error=BlastX.%J.err
+
+
+
+module load biodata/1.0
+
+module load blast/2.7
+
+cd $WORK/<project\_folder>
+
+cp $BLAST/nr.\* /scratch/
+cp input\_reads.fasta /scratch/
+
+blastx -query /scratch/input\_reads.fasta -db /scratch/nr -outfmt 6 -out
+/scratch/blastx\_output.alignments -num\_threads
+$SLURM\_NTASKS\_PER\_NODE
+
+cp /scratch/blastx\_output.alignments $WORK/<project\_folder>
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[cb\_blast\_module.xsl](attachments/8193291/8127544.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/8127545.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[cb\_blastn\_biodata.xsl](attachments/8193291/16521350.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/17039409.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/17039457.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/17039505.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/17039553.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/17039603.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/17039663.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/17039865.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/17039913.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/17039961.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/17040043.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/17040131.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/17040213.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/17040357.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/17040437.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/17040485.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/17040567.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/17040710.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/17041089.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/17041155.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/17041226.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/17041557.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/17041609.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/17041784.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/17041912.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/17041999.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/17042089.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/17042174.xml) (text/xml)
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+[tusker\_modules.xml](attachments/8193291/30443207.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/30443334.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/30443544.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/30443647.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/30443763.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/30443868.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/30443973.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/30444084.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/30444184.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/30444308.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/30444421.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/30444573.xml) (text/xml)
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+[tusker\_modules.xml](attachments/8193291/30444724.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/30444928.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/30444992.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/30445098.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+[tusker\_modules.xml](attachments/8193291/30445427.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/30445530.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/30445745.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/30445957.xml) (text/xml)
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/30446915.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/30447077.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/30447139.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/30447248.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/30447472.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/30447576.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/30447649.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/30447749.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/30447984.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/30448084.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/30448290.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/30448433.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/30448660.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/30448763.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/30448870.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/30448978.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/33685599.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/33685710.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/33685822.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/33685927.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/33686064.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/33686168.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/33686307.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/33687843.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/33688451.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/33689776.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/33689996.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/35324036.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/35324146.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/35324616.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/35324906.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/35325638.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193291/35325453.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193291/35325479.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193291/35325498.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193291/35325531.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193291/35325868.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/35325751.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/35326738.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193291/35325887.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193291/35325915.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193291/35325934.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193291/35325965.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193291/35326023.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193291/35326094.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193291/35326207.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193291/35326309.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193291/35326403.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193291/35326431.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193291/35326499.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193291/35326549.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193291/35326588.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193291/35326639.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193291/35326661.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193291/35326819.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193291/16521353.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193291/35326896.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193291/35326931.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193291/35326950.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193291/35327032.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193291/35325367.xml) (text/xml)
+
+Document generated by Confluence on Oct 24, 2018 14:49
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/bioinformatics_tools/alignment_tools/blat.md b/content/guides/running_applications/bioinformatics_tools/alignment_tools/blat.md
new file mode 100644
index 00000000..e8c43296
--- /dev/null
+++ b/content/guides/running_applications/bioinformatics_tools/alignment_tools/blat.md
@@ -0,0 +1,110 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Running Applications](Running-Applications_7471153.html)
+5. [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
+6. [Alignment Tools](Alignment-Tools_8193288.html)
+
+<span id="title-text"> HCC-DOCS : BLAT </span>
+==============================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified by
+<span class="editor"> Natasha Pavlovikj</span> on Dec 12, 2016
+
+| Name | Version | Resource |
+|------|---------|----------|
+| blat | 35x1 | Tusker |
+
+| | | |
+|------|------|-------|
+| blat | 35x1 | Crane |
+
+<span style="line-height: 1.4285715;">
+</span>
+
+<span style="line-height: 1.4285715;">BLAT is a pairwise alignment tool
+similar to BLAST. It is more accurate and about 500 times faster than
+the existing tools for mRNA/DNA alignments and it is about 50 times
+faster with protein/protein alignments. BLAT accepts short and long
+query and database sequences as input files.</span>
+
+The basic usage of BLAT is:
+
+**General BLAT Usage**
+
+``` syntaxhighlighter-pre
+blat database query output_alignment.txt [options]
+```
+
+where **database** is the name of the database used for the alignment,
+**query** is the name of the input file of sequence data in
+fasta/nib/2bit format, and **output\_alignment.txt** is the output
+alignment file. Additional parameters for BLAT alignment can be found in
+the
+manual: <a href="http://genome.ucsc.edu/goldenPath/help/blatSpec.html" class="external-link">http://genome.ucsc.edu/goldenPath/help/blatSpec.html</a>,
+or by using
+
+**Additional BLAT Options**
+
+``` syntaxhighlighter-pre
+[<username>@login.tusker~]$ blat
+```
+
+Running BLAT on Tusker with query file **input\_reads.fasta** and
+database **db.fa** is shown below:
+
+**blat\_alignment.submit**
+
+\#!/bin/sh
+\#SBATCH --job-name=Blat
+\#SBATCH --nodes=1
+\#SBATCH --ntasks-per-node=1
+\#SBATCH --time=168:00:00
+\#SBATCH --mem=50gb
+\#SBATCH --output=Blat.%J.out
+\#SBATCH --error=Blat.%J.err
+
+
+
+| |
+|-----------------------|
+| module load blat/35x1 |
+
+blat db.fa input\_reads.fasta output\_alignment.txt
+
+Although BLAT is a single threaded program (**\#SBATCH --nodes=1**,
+**\#SBATCH --ntasks-per-node=1**) it is still much faster than the other
+alignment tools.
+
+
+
+**BLAT Output**
+
+BLAT output is a list containing the following information: *the score
+of the alignment*, *the region of query sequence that matches the
+database sequence*, *the size of the query sequence*, *the level of
+identity as a percentage of the alignment* and *the chromosome and
+position that the query sequence maps to*.
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[cb\_blat\_module.xsl](attachments/8193292/8127546.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_blat\_version.xsl](attachments/8193292/8127547.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193292/8127548.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_blat\_version.xsl](attachments/8193292/8127549.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193292/8127550.xml)
+(application/octet-stream)
+
+Document generated by Confluence on Oct 24, 2018 14:50
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/bioinformatics_tools/alignment_tools/bowtie.md b/content/guides/running_applications/bioinformatics_tools/alignment_tools/bowtie.md
new file mode 100644
index 00000000..03530f80
--- /dev/null
+++ b/content/guides/running_applications/bioinformatics_tools/alignment_tools/bowtie.md
@@ -0,0 +1,3289 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Running Applications](Running-Applications_7471153.html)
+5. [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
+6. [Alignment Tools](Alignment-Tools_8193288.html)
+
+<span id="title-text"> HCC-DOCS : Bowtie </span>
+================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified by
+<span class="editor"> Natasha Pavlovikj</span> on Dec 12, 2016
+
+| Name | Version | Resource |
+|--------|---------|----------|
+| bowtie | 0.12.8 | Tusker |
+| bowtie | 0.12.9 | Tusker |
+| bowtie | 1.0.0 | Tusker |
+| bowtie | 1.1.2 | Tusker |
+
+| | | |
+|--------|-------|-------|
+| bowtie | 1.0 | Crane |
+| bowtie | 1.1.2 | Crane |
+
+
+
+Bowtie
+(<a href="http://bowtie-bio.sourceforge.net/index.shtml" class="external-link">http://bowtie-bio.sourceforge.net/index.shtml</a>)
+is an ultrafast and memory-efficient aligner for large sets of
+sequencing reads to a reference genome. Bowtie indexes the genome with a
+Burrows-Wheeler index to keep its memory footprint small. Bowtie also
+supports usage of multiple processors to achieve greater alignment
+speed.
+
+The first and basic step of running Bowtie is to build and format an
+index from the reference genome. The basic usage of this command
+**bowtie-build** is:
+
+**General Bowtie-Build Usage**
+
+``` syntaxhighlighter-pre
+bowtie-build input_reference.fasta index_prefix
+```
+
+where **input\_reference.fasta** is an input file of sequence reads in
+fasta format, and **index\_prefix** is the prefix of the generated index
+files.
+
+After the index of the reference genome is generated, the next step is
+to align the reads. The basic usage of bowtie is:
+
+**General Bowtie Usage**
+
+``` syntaxhighlighter-pre
+bowtie [-q|-f|-r|-c] index_prefix [-1 input_reads_pair_1.[fasta|fastq] -2 input_reads_pair_2.[fasta|fastq] | input_reads.[fasta|fastq]] [options]
+```
+
+where **index\_prefix** is the generated index using the
+**bowtie-build** command, and **options** are optional parameters that
+can be found in the Bowtie
+manual: <a href="http://bowtie-bio.sourceforge.net/manual.shtml" class="external-link">http://bowtie-bio.sourceforge.net/manual.shtml</a>.
+Bowtie supports both single-end (**input\_reads.\[fasta\|fastq\]**) and
+paired-end
+(i**nput\_reads\_pair\_1.\[fasta\|fastq\]**, **input\_reads\_pair\_2.\[fasta\|fastq\]**)
+files in fasta or fastq format. The format of the input files also needs
+to be specified by using the following flags: **-q** (fastq files),
+**-f** (fasta files), **-r**(raw one-sequence per line), or **-c**
+(sequences given on command line).
+
+An example of how to run Bowtie alignment on Tusker with single-end
+fastq file and 8 CPUs is shown below:
+
+**bowtie\_alignment.submit**
+
+\#!/bin/sh
+\#SBATCH --job-name=Bowtie
+\#SBATCH --nodes=1
+\#SBATCH --ntasks-per-node=8
+\#SBATCH --time=168:00:00
+\#SBATCH --mem=50gb
+\#SBATCH --output=Bowtie.%J.out
+\#SBATCH --error=Bowtie.%J.err
+
+
+
+| |
+|------------------------|
+| module load bowtie/1.1 |
+
+bowtie -q index\_prefix input\_reads.fastq -p $SLURM\_NTASKS\_PER\_NODE
+> bowtie\_alignments.sam
+
+
+
+**Bowtie Output**
+
+Bowtie output is an alignment file in SAM format, where one line is one
+alignment. Each line is a collection of 8 fields separated by tabs. The
+fields are: *name of the aligned reads*, r*eference strand aligned to*,
+*name of reference sequence where the alignment occurs*, *0-based offset
+into the forward reference strand where leftmost character of the
+alignment occurs*, *read sequence*, *read qualities*, *the number of
+other instances where the same sequence is aligned against the same
+reference characters*, and *comma-separated list of mismatch
+descriptors*.
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[cb\_bowtie\_module.xsl](attachments/8193293/8127551.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_bowtie\_version.xsl](attachments/8193293/8127552.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_bowtie\_version.xsl](attachments/8193293/8127554.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193293/11637641.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193293/11637449.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193293/11637481.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193293/11637513.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193293/11637550.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193293/11637598.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193293/11637720.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193293/11637685.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193293/11637925.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193293/11637747.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193293/11637774.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193293/11637801.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193293/11637856.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193293/11638118.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193293/11638016.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193293/11638091.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193293/11638161.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193293/11638231.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193293/11638204.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193293/12550247.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193293/12386337.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193293/13041702.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193293/12550295.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193293/12550345.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193293/13041756.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193293/13041800.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193293/13041844.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193293/13041873.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193293/13041916.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193293/13042008.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193293/13041978.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193293/13042134.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193293/13042037.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193293/13042064.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193293/13042091.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193293/13042176.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193293/13042258.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193293/13042215.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193293/13042382.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193293/13042307.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193293/13042350.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193293/13042453.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193293/13042409.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193293/13042480.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193293/13042523.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193293/13042550.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193293/13042620.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193293/13042577.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193293/13042693.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193293/13042666.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193293/13598790.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193293/13598747.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193293/13598942.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193293/13599012.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193293/13598969.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193293/13599148.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193293/13599367.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193293/13599176.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193293/13599203.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193293/13599287.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193293/14057505.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193293/13599423.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193293/13599466.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193293/13599526.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193293/14057628.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193293/14057585.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193293/14057698.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193293/14057671.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193293/14057749.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193293/14057776.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193293/14057851.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193293/14057808.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193293/14057966.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193293/14057938.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193293/14417986.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193293/14418013.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193293/14418232.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193293/14418040.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193293/14418067.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193293/14418118.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193293/14418145.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193293/14418184.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193293/15171808.xml)
+(application/octet-stream)
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+(application/octet-stream)
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+[tusker\_modules.xml](attachments/8193293/15171853.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193293/15171881.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193293/15172012.xml)
+(application/octet-stream)
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+[crane\_modules.xml](attachments/8193293/15171967.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193293/15172040.xml)
+(application/octet-stream)
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+[tusker\_modules.xml](attachments/8193293/15172413.xml)
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+[crane\_modules.xml](attachments/8193293/15172069.xml)
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+[tusker\_modules.xml](attachments/8193293/11637419.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193293/17044366.xml) (text/xml)
+
+Document generated by Confluence on Oct 24, 2018 14:50
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/bioinformatics_tools/alignment_tools/bowtie2.md b/content/guides/running_applications/bioinformatics_tools/alignment_tools/bowtie2.md
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--- /dev/null
+++ b/content/guides/running_applications/bioinformatics_tools/alignment_tools/bowtie2.md
@@ -0,0 +1,954 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Running Applications](Running-Applications_7471153.html)
+5. [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
+6. [Alignment Tools](Alignment-Tools_8193288.html)
+
+<span id="title-text"> HCC-DOCS : Bowtie2 </span>
+=================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified by
+<span class="editor"> Natasha Pavlovikj</span> on Dec 12, 2016
+
+| Name | Version | Resource |
+|--------|-------------|----------|
+| bowtie | 2.0.0-beta6 | Tusker |
+| bowtie | 2.1.0 | Tusker |
+| bowtie | 2.2.6 | Tusker |
+| bowtie | 2.3.4 | Tusker |
+
+| | | |
+|--------|-------|-------|
+| bowtie | 2.2.6 | Crane |
+| bowtie | 2.3.4 | Crane |
+
+
+
+Bowtie2
+(<a href="http://bowtie-bio.sourceforge.net/bowtie2/index.shtml" class="external-link">http://bowtie-bio.sourceforge.net/bowtie2/index.shtml</a>)
+is an ultrafast and memory-efficient tool for aligning sequencing reads
+to long reference sequences. Although Bowtie and Bowtie2 are both fast
+read aligners, there are few main differences between them:
+
+- Bowtie2 supports gapped alignment with affine gap penalties, without
+ restrictions on the number of gaps and gap lengths.
+- Bowtie supports reads longer than 50bp and is generally faster, more
+ sensitive, and uses less memory than Bowtie.
+- Bowtie support only end-to-end alignments, while Bowtie2 supports
+ both end-to-end and local alignment.
+- Bowtie has an upper limit on read length of around 1,000 bp, while
+ Bowtie2 does not have any.
+- Bowtie2's paired-end alignment is more flexible that Bowtie's.
+- Bowtie2 does not align colorspace reads.
+- Bowtie and Bowtie2 indices are not compatible.
+
+Same as Bowtie, the first and basic step of running Bowtie2 is to build
+a Bowtie2 index from a reference genome sequence. The basic usage of the
+command **bowtie2-build** is:
+
+**General Bowtie2-Build Usage**
+
+``` syntaxhighlighter-pre
+bowtie2-build -f input_reference.fasta index_prefix
+```
+
+where **input\_reference.fasta** is an input file of sequence reads in
+fasta format, and **index\_prefix** is the prefix of the generated index
+files. Beside the option **-f** that is used when the reference input
+file is a fasta file, the option **-c** can be used when the reference
+sequences are given on the command line.
+
+The command **bowtie2** takes a Bowtie2 index and set of sequencing read
+files and outputs set of alignments in SAM format. The general
+**bowtie2** usage is:
+
+**General Bowtie2 Usage**
+
+``` syntaxhighlighter-pre
+bowtie2 -x index_prefix [-q|--qseq|-f|-r|-c] [-1 input_reads_pair_1.[fasta|fastq] -2 input_reads_pair_2.[fasta|fastq] | -U input_reads.[fasta|fastq]] -S bowtie2_alignments.sam [options]
+```
+
+where **index\_prefix** is the generated index using
+the **bowtie2-build** command, and **options** are optional parameters
+that can be found in the Bowtie2
+manual: <a href="http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml" class="external-link">http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml</a>. Bowtie2
+supports both single-end (**input\_reads.\[fasta\|fastq\]**) and
+paired-end
+(i**nput\_reads\_pair\_1.\[fasta\|fastq\]**, **input\_reads\_pair\_2.\[fasta\|fastq\]**)
+files in fasta or fastq format. The format of the input files also needs
+to be specified by using one of the following flags: **-q** (fastq
+files), **--qseq** (Illumina's qseq format), **-f** (fasta files),
+**-r** (raw one sequence per line), or **-c** (sequences given on
+command line).
+
+An example of how to run Bowtie2 local alignment on Tusker with
+paired-end fasta files and 8 CPUs is shown below:
+
+**bowtie2\_alignment.submit**
+
+\#!/bin/sh
+\#SBATCH --job-name=Bowtie2
+\#SBATCH --nodes=1
+\#SBATCH --ntasks-per-node=8
+\#SBATCH --time=168:00:00
+\#SBATCH --mem=50gb
+\#SBATCH --output=Bowtie2.%J.out
+\#SBATCH --error=Bowtie2.%J.err
+
+
+
+| |
+|------------------------|
+| module load bowtie/2.3 |
+
+bowtie2 -x index\_prefix -f -1 input\_reads\_pair\_1.fasta -2
+input\_reads\_pair\_2.fasta -S bowtie2\_alignments.sam --local -p
+$SLURM\_NTASKS\_PER\_NODE
+
+
+
+**Bowtie2 Output**
+
+Bowtie2 outputs alignments in SAM format that can further be manipulated
+with different tools, like SAMtools and GATK. Each line from the file
+describes an alignment and is a collection of at least 12 fields
+separated by tabs. Detailed information about Bowtie2 output fields can
+be found in the Bowtie2 manual.
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[cb\_bowtie2\_module.xsl](attachments/8193294/8127556.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_bowtie2\_version.xsl](attachments/8193294/8127557.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/8127558.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_bowtie2\_version.xsl](attachments/8193294/8127559.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/8127560.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/17044383.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/17044419.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/17044487.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/17044523.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/17044583.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/17044619.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/17044680.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/17044716.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/17044780.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/17044816.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/17044933.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/17044969.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/17047002.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/17047038.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/18546778.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/18546708.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/18546851.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/18546913.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/18547016.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/18546984.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/18547220.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/18547089.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/18547158.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/18547343.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/18547272.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/18547409.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/18547489.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/18547454.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/18547555.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/18547590.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/18547655.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/18547690.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/18547765.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/18547800.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/18547926.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/18547861.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/18547961.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/18548026.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/18548125.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/18548090.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/18548209.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/18548244.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/18548309.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/18548345.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/18548455.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/18548490.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/18548655.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/18548577.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/18548690.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/18548755.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/18548790.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/18548915.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/18548850.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/18548991.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/18548956.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/18549075.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/20709462.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/20709424.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/20709528.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/20709564.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/21069840.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/21069879.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/21069958.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/21069997.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/21070096.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/21070135.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/21070208.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/21070247.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/21070337.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/21070485.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/21070405.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/21070446.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/21070549.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/21070588.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/21070668.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/21070707.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/21070769.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/21070808.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/21070918.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/21071002.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/21070963.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/21071074.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/21071113.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/21071185.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/21071294.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/21071255.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/21071356.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/21071395.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/21071518.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/21071557.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/21071653.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/21071693.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/21071757.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/21071796.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/21071860.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/21071899.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/21071960.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/21071999.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/21072060.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/21072140.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/21072101.xml) (text/xml)
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/33689785.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/33689974.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/33690005.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/35323983.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/35324045.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/35324093.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/35324155.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/35324431.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/35324625.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/35324561.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/35324851.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/35324915.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/35325016.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/35325647.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/35325185.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/35325228.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/35325271.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/35325578.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/35325695.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/35325760.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/35326156.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/35326747.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/35326682.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193294/17044368.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193294/17044369.xml) (text/xml)
+
+Document generated by Confluence on Oct 24, 2018 14:50
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/bioinformatics_tools/alignment_tools/bwa/_index.md b/content/guides/running_applications/bioinformatics_tools/alignment_tools/bwa/_index.md
new file mode 100644
index 00000000..46989c4e
--- /dev/null
+++ b/content/guides/running_applications/bioinformatics_tools/alignment_tools/bwa/_index.md
@@ -0,0 +1,906 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Running Applications](Running-Applications_7471153.html)
+5. [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
+6. [Alignment Tools](Alignment-Tools_8193288.html)
+
+<span id="title-text"> HCC-DOCS : BWA </span>
+=============================================
+
+Created by <span class="author"> Adam Caprez</span> on Sep 04, 2014
+
+| Name | Version | Resource |
+|------|---------|----------|
+| bwa | 0.6.2 | Tusker |
+| bwa | 0.7 | Tusker |
+
+| | | |
+|-----|-------|-------|
+| bwa | 0.6.2 | Crane |
+| bwa | 0.7 | Crane |
+
+
+
+BWA (Burrows-Wheeler Aligner) is a software package for mapping
+relatively short nucleotide sequences against a long reference
+sequence. BWA is slower than Bowtie, but allows indels in the alignment.
+
+The basic usage of BWA is:
+
+**General BWA Usage**
+
+``` syntaxhighlighter-pre
+bwa COMMAND [options]
+```
+
+where **COMMAND** is one of the available BWA commands**:**
+
+- **index**: index sequences in the FASTA format
+- **mem**: BWA-MEM algorithm
+- **fastmap**: identify super-maximal exact matches
+- **pemerge**: merge overlapping paired ends (EXPERIMENTAL)
+- **aln**: gapped/ungapped alignment
+- **samse**: generate alignment (single ended)
+- **sampe**: generate alignment (paired ended)
+- **bwasw**: BWA-SW for long queries
+- **fa2pac**: convert FASTA to PAC format
+- **pac2bwt**: generate BWT from PAC
+- **pac2bwtgen**: alternative algorithm for generating BWT
+- **bwtupdate**: update .bwt to the new format
+- **bwt2sa**: generate SA from BWT and Occ
+
+BWA supports three alignment algorithms: **mem**, **bwasw**, and
+**aln**/**samse**/**sampe**. **BWA mem** is the latest algorithm, and is
+faster, more accurate and has better performance than **BWA bwasw** and
+**BWA aln**/**samse**/**sampe**. Therefore, if there are not any
+specific reasons, **BWA mem** is recommended for first-time users.
+
+For detailed description and more information on a specific command,
+just type:
+
+**General BWA COMMAND Options**
+
+``` syntaxhighlighter-pre
+[<username>@login.tusker~]$ bwa COMMAND
+```
+
+or check the BWA
+manual: <a href="http://bio-bwa.sourceforge.net/bwa.shtml" class="external-link">http://bio-bwa.sourceforge.net/bwa.shtml</a>.
+
+The page [Running BWA Commands](Running-BWA-Commands_8193296.html) shows
+how to run BWA on HCC.
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_bwa\_version.xsl](attachments/8193295/8127561.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/8127562.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_bwa\_version.xsl](attachments/8193295/8127563.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/8127564.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/17044384.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/17044421.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/17044488.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/17044525.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/17044584.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/17044621.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/17044681.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/17044718.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/17044781.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/17044818.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/17044934.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/17044971.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/17047003.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/17047040.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/18546779.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/18546710.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/18546853.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/18546914.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/18547018.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/18546985.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/18547221.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/18547091.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/18547160.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/18547345.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/18547273.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/18547410.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/18547491.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/18547455.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/18547556.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/18547592.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/18547656.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/18547692.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/18547766.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/18547802.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/18547927.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/18547863.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/18547963.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/18548027.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/18548127.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/18548091.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/18548210.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/18548246.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/18548310.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/18548347.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/18548456.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/18548492.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/18548656.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/18548579.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/18548692.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/18548756.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/18548792.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/18548916.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/18548852.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/18548993.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/18548957.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/18549076.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/20709464.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/20709425.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/20709529.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/20709566.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/21069841.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/21069881.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/21069959.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/21069999.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/21070097.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/21070137.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/21070209.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/21070249.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/21070338.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/21070487.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/21070406.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/21070447.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/21070550.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/21070590.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/21070669.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/21070709.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/21070770.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/21070810.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/21070919.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/21071004.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/21070964.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/21071075.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/21071115.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/21071186.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/21071296.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/21071256.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/21071357.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/21071397.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/21071519.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/21071559.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/21071654.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/33686075.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/33686147.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/33686179.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/33686286.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/33686318.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/33687822.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/33687854.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/33688428.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/33688463.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/33689755.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/33689787.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/33689975.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/33690007.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/35323984.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/35324047.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/35324094.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/35324157.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/35324432.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/35324627.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/35324562.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/35324852.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/35324917.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/35325017.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/35325649.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/35325186.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/35325229.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/35325272.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/35325579.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/35325696.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/35325762.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/35326157.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/35326749.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/35326683.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193295/17044370.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193295/17044371.xml) (text/xml)
+
+Document generated by Confluence on Oct 24, 2018 14:50
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/bioinformatics_tools/alignment_tools/bwa/running_bwa_commands.md b/content/guides/running_applications/bioinformatics_tools/alignment_tools/bwa/running_bwa_commands.md
new file mode 100644
index 00000000..f9a06460
--- /dev/null
+++ b/content/guides/running_applications/bioinformatics_tools/alignment_tools/bwa/running_bwa_commands.md
@@ -0,0 +1,322 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Running Applications](Running-Applications_7471153.html)
+5. [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
+6. [Alignment Tools](Alignment-Tools_8193288.html)
+7. [BWA](BWA_8193295.html)
+
+<span id="title-text"> HCC-DOCS : Running BWA Commands </span>
+==============================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified by
+<span class="editor"> Natasha Pavlovikj</span> on Dec 12, 2016
+
+**BWA Index:**
+
+The first step of using BWA is to make an index of the reference genome
+in fasta format. The basic usage of the **bwa index** is:
+
+**General BWA Index Usage**
+
+``` syntaxhighlighter-pre
+bwa index [-a bwtsw|is] input_reference.fasta index_prefix
+```
+
+where **input\_reference.fasta** is an input file of the reference
+genome in fasta format, and **index\_prefix** is the prefix of the
+generated index files. The option **-a** is required and can have two
+values: **bwtsw** (does not work for short genomes) and **is** (does not
+work for long genomes). Therefore, this value is chosen according to the
+length of the genome.
+
+**
+**
+
+**BWA Mem:**
+
+The **bwa mem** algorithm is one of the three algorithms provided by
+BWA. It performs local alignment and produces alignments for different
+part of the query sequence.
+
+**General BWA Mem Usage**
+
+``` syntaxhighlighter-pre
+bwa mem index_prefix [input_reads.fastq|input_reads_pair_1.fastq input_reads_pair_2.fastq] [options]
+```
+
+where **index\_prefix** is the index for the reference genome generated
+from **bwa index**, and **input\_reads.fastq**,
+**input\_reads\_pair\_1.fastq**, **input\_reads\_pair\_2.fastq** are the
+input files of sequencing data that can be single-end or paired-end
+respectively. Additional **options** for **bwa mem** can be found in the
+BWA manual.
+
+Simple SLURM script for running **bwa mem** on Tusker with paired-end
+fastq input data, **index\_prefix** as reference genome index, SAM
+output file and 8 CPUs is shown below:
+
+**bwa\_mem.submit**
+
+\#!/bin/sh
+\#SBATCH --job-name=Bwa\_Mem
+\#SBATCH --nodes=1
+\#SBATCH --ntasks-per-node=8
+\#SBATCH --time=168:00:00
+\#SBATCH --mem=50gb
+\#SBATCH --output=BwaMem.%J.out
+\#SBATCH --error=BwaMem.%J.err
+
+
+
+| |
+|---------------------|
+| module load bwa/0.7 |
+
+bwa mem index\_prefix input\_reads\_pair\_1.fastq
+input\_reads\_pair\_2.fastq -t $SLURM\_NTASKS\_PER\_NODE >
+bwa\_mem\_alignments.sam
+
+
+
+****BWA Bwasw:****
+
+The **bwa bwasw** algorithm is another algorithm provided by BWA. For
+input files with single-end reads it aligns the query sequences. For
+input files with paired-ends reads it performs paired-end alignment that
+only works for Illumina reads. An example of **bwa bwasw** for
+single-end input file **input-reads.fasta** in fasta format and output
+file **bwa\_bwasw\_alignments.sam** where the alignments are stored, is
+shown below:
+
+**General BWA Bwasw Usage**
+
+``` syntaxhighlighter-pre
+bwa bwasw index_prefix input_reads.fasta -t $SLURM_NTASKS_PER_NODE > bwa_bwasw_alignments.sam
+```
+
+**
+**
+
+**BWA Aln:**
+
+The third BWA algorithm, **bwa aln**, aligns the input file of sequence
+data to the reference genome. In addition, there is an example of
+running **bwa aln** with single-end **input\_reads.fasta** input file
+and 8 CPUs:
+
+**General BWA Aln Usage**
+
+``` syntaxhighlighter-pre
+bwa aln index_prefix input_reads.fasta -0 -t $SLURM_NTASKS_PER_NODE > bwa_aln_alignments.sai
+```
+
+The command **bwa samse** uses the **bwa\_aln\_alignments.sai** output
+form **bwa aln** in order to generate SAM file from the alignments for
+single-end reads.
+
+**General BWA Samse Usage**
+
+``` syntaxhighlighter-pre
+bwa samse -f bwa_aln_alignments.sam index_prefix bwa_aln_alignments.sai input_reads.fasta
+```
+
+The command **bwa sampe** uses the **bwa\_aln\_alignments.sai** output
+form **bwa aln** in order to generate SAM file from the alignments for
+paired-end reads.
+
+**General BWA Sampe Usage**
+
+``` syntaxhighlighter-pre
+bwa samse -f bwa_aln_alignments.sam index_prefix bwa_aln_alignments_pair_1.sai bwa_aln_alignments_pair_2.sai input_reads_pair_1.fasta input_reads_pair_2.fasta
+```
+
+****
+****
+
+**BWA Fastmap:**
+
+The command **bwa fastmap** identifies and outputs super-maximal exact
+matches (SMEMs).
+
+**General BWA Fastmap Usage**
+
+``` syntaxhighlighter-pre
+bwa fastmap index_prefix input_reads.fasta > bwa_fastmap.matches
+```
+
+**
+**
+
+**BWA Pemerge:**
+
+The command **bwa pemerge** merges overlapping paired ends and can print
+either only the merged reads or the unmerged ones. An example of **bwa
+pemerge** of **input\_reads\_pair\_1.fastq**
+and **input\_reads\_pair\_2.fastq** with 8 CPUs and output
+file **output\_reads\_merged.fastq** that contains only the merged reads
+is shown below:
+
+**General BWA Pemerge Usage**
+
+``` syntaxhighlighter-pre
+bwa pemerge -m input_reads_pair_1.fastq input_reads_pair_2.fastq -t $SLURM_NTASKS_PER_NODE > output_reads_merged.fastq
+```
+
+
+
+**BWA Fa2pac:**
+
+The command **bwa fa2pac** converts fasta to pac files.
+
+**General BWA Pac2pac Usage**
+
+``` syntaxhighlighter-pre
+bwa fa2pac input_reads.fasta pac_prefix
+```
+
+
+
+**BWA Pac2bwt and **BWA Pac2bwtgen**:**
+
+The commands **bwa pac2bwt** and **bwa pac2bwtgen** convert pac to bwt
+files.
+
+**General BWA Pac2bwt Usage**
+
+``` syntaxhighlighter-pre
+bwa pac2bwt input_reads.pac output_reads.bwt
+```
+
+**General BWA Pac2bwtgen Usage**
+
+``` syntaxhighlighter-pre
+bwa pac2bwtgen input_reads.pac output_reads.bwt
+```
+
+
+
+**BWA Bwtupdate:**
+
+The command **bwa bwtupdate** updates bwt files to the new format.
+
+**General BWA Bwtupdate Usage**
+
+``` syntaxhighlighter-pre
+bwa bwtupdate input_reads.bwt
+```
+
+**
+**
+
+**BWA Bwt2sa:**
+
+The command **bwa bwt2sa** generates sa files from bwt and Occ files.
+
+**General BWA Bwt2sa Usage**
+
+``` syntaxhighlighter-pre
+bwa bwt2sa input_reads.bwt output_reads.sa
+```
+
+
+
+**Useful Information**
+
+In order to test the scalability of BWA (bwa/0.7) on Crane, we used two
+paired-end input fastq files: **large\_1.fastq** and **large\_2.fastq**,
+and one single-end input fasta file, **large.fasta**. Some statistics
+about the input files and the time and memory resources required
+for *bwa mem* are shown on the table below:
+
+
+
+**total \# of sequences**
+
+**total size in MB**
+
+<span style="color: rgb(0,0,0);">\# of used CPUs</span>
+
+running time for 4 CPUs
+
+required memory for 4 CPUs
+
+<span style="color: rgb(0,0,0);">\# of used CPUs</span>
+
+running time for 8 CPUs
+
+required memory for 8 CPUs
+
+<span style="color: rgb(0,0,0);">\# of used CPUs</span>
+
+running time for 16 CPUs
+
+required memory for 16 CPUs
+
+**large\_1.fastq**
+
+10,174,715
+
+3,376 MB
+
+4
+
+\~ 35 minutes
+
+\~ 12 GB
+
+8
+
+\~ 18.5 minutes
+
+\~ 18 GB
+
+16
+
+\~ 10 minutes
+
+\~ 19 GB
+
+**large\_2.fastq**
+
+10,174,715
+
+3,376 MB
+
+**large.fasta**
+
+592,593
+
+836 MB
+
+4
+
+\~ 5.5 minutes
+
+\~ 3 GB
+
+8
+
+\~ 3 minutes
+
+\~ 4 GB
+
+16
+
+\~ 2 minutes
+
+\~ 6.2 GB
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[cb\_bwa\_module.xsl](attachments/8193296/8127565.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193296/8127566.xml)
+(application/octet-stream)
+
+Document generated by Confluence on Oct 24, 2018 14:50
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/bioinformatics_tools/alignment_tools/clustal_omega.md b/content/guides/running_applications/bioinformatics_tools/alignment_tools/clustal_omega.md
new file mode 100644
index 00000000..6c05d799
--- /dev/null
+++ b/content/guides/running_applications/bioinformatics_tools/alignment_tools/clustal_omega.md
@@ -0,0 +1,201 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Running Applications](Running-Applications_7471153.html)
+5. [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
+6. [Alignment Tools](Alignment-Tools_8193288.html)
+
+<span id="title-text"> HCC-DOCS : Clustal Omega </span>
+=======================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified by
+<span class="editor"> Natasha Pavlovikj</span> on Dec 12, 2016
+
+| Name | Version | Resource |
+|---------------|---------|----------|
+| clustal-omega | 1.2 | Tusker |
+
+| | | |
+|---------------|-----|-------|
+| clustal-omega | 1.2 | Crane |
+
+
+
+Clustal Omega
+(<a href="http://www.clustal.org/omega/" class="external-link">http://www.clustal.org/omega/</a>)
+is a general purpose multiple sequence alignment (MSA) tool used mainly
+with protein, as well as DNA and RNA sequences. Clustal Omega is fast
+and scalable aligner that can align datasets of hundreds of thousands of
+sequences in reasonable time.
+
+The general usage of Clustal Omega is:
+
+**General Clustal Omega Usage**
+
+``` syntaxhighlighter-pre
+clustalo -i input_file.fasta -o output_file.fasta [options]
+```
+
+where **input\_file.fasta** is the multiple sequence input file in
+*fasta* format, and **output\_file.fasta** is the multiple sequence
+alignment output file in *fasta* format.
+Clustal Omega accepts 3 types of sequence input files:
+
+- sequence file with aligned/unaligned sequences
+
+<!-- -->
+
+- multiple alignment in a file/profile of aligned sequences
+
+<!-- -->
+
+- Hidden Markov Model (HMM)
+
+These input files must contain at least 2 sequences and must be in one
+of the following MSA file formats: **a2m**, **fa\[sta\]**,
+**clu\[stal\]**, **msf**, **phy\[lip\]**, **selex**, **st\[ockholm\]**,
+**vie\[nna\]**. Moreover, if not specified, the generated output file is
+in *fasta* format.
+
+More Clustal Omega options can be found by typing:
+
+**Additional Clustal Omega Options**
+
+``` syntaxhighlighter-pre
+[<username>@login.tusker~]$ clustalo -h
+```
+
+
+Running Clustal Omega on Tusker with input
+file **input\_reads.fasta** with **8 threads** and **10GB memory** is
+shown below:
+
+**clustal\_omega.submit**
+
+\#!/bin/sh
+\#SBATCH --job-name=Clustal\_Omega
+\#SBATCH --nodes=1
+\#SBATCH --ntasks-per-node=8
+\#SBATCH --time=10:00:00
+\#SBATCH --mem=10gb
+\#SBATCH --output=ClustalOmega.%J.out
+\#SBATCH --error=ClustalOmega.%J.err
+
+
+
+| |
+|-------------------------------|
+| module load clustal-omega/1.2 |
+
+clustalo -i input\_reads.fasta -o output\_msa.sto --outfmt=st
+--threads=$SLURM\_NTASKS\_PER\_NODE
+
+The output file **output\_msa.sto** contains the resulting multiple
+sequence alignments in Stockholm format (**--outfmt=st**).
+
+Moreover, if you change the command above with:
+
+**Clustal Omega with De-align Option**
+
+``` syntaxhighlighter-pre
+clustalo -i input_reads.sto --dealign -v
+```
+
+Clustal Omega will read the input file in Stockholm format, de-align the
+sequences, and then re-align them, printing progress report in meanwhile
+(**-v**). Because it is not specified, the output will be in the default
+**fasta** format.
+
+
+
+**Clustal Omega Output**
+
+The basic Clustal Omega output produces one alignment file in the
+specified output format. More intermediate outputs can be generated
+using specific Clustal Omega options, such
+as: **--distmat-out=<file>** (*pairwise distance matrix output
+file*) and **--guidetree-out=<file>** (*guide tree output file*).
+
+**
+Useful Information**
+
+In order to test the Clustal Omega performance on Tusker, we used three
+DNA and protein input fasta files: **data\_1. fasta, data\_2. fasta,
+data\_3.fasta**. Some statistics about the input files and the time and
+memory resources required for Clustal Omega are shown on the table
+below:
+
+<table style="width:100%;">
+<colgroup>
+<col style="width: 14%" />
+<col style="width: 14%" />
+<col style="width: 14%" />
+<col style="width: 14%" />
+<col style="width: 14%" />
+<col style="width: 14%" />
+<col style="width: 14%" />
+</colgroup>
+<thead>
+<tr class="header">
+<th> </th>
+<th><p><strong>total # of sequences</strong></p></th>
+<th><p><strong>average sequence length</strong></p></th>
+<th><p><strong>total size in MB</strong></p></th>
+<th><p><strong>Clustal Omega required time</strong></p></th>
+<th><p><strong>Clustal Omega required memory</strong></p></th>
+<th># of used CPUs</th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td><p><strong>data_1.fasta</strong></p></td>
+<td><p>1,200</p></td>
+<td><p>510.17</p></td>
+<td><p>641 KB</p></td>
+<td><p>~ 5 minutes</p></td>
+<td><span>~ 65 MB</span></td>
+<td>8</td>
+</tr>
+<tr class="even">
+<td><p><strong>data_2.fasta</strong></p></td>
+<td><p>5,715</p></td>
+<td><p>174.20</p></td>
+<td><p>1,100 KB</p></td>
+<td>~ 5 minutes</td>
+<td><p>~ 140 MB</p></td>
+<td><p>8</p></td>
+</tr>
+<tr class="odd">
+<td><p><strong>data_3.fasta</strong></p></td>
+<td><p>93,675</p></td>
+<td><p>94.29</p></td>
+<td><p>11,000 KB</p></td>
+<td><p>~ 30 minutes</p></td>
+<td><p>~ 2 GB</p></td>
+<td><p>8</p></td>
+</tr>
+</tbody>
+</table>
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_clustal\_omega\_version.xsl](attachments/9470379/9863812.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[cb\_clustal\_omega\_module.xsl](attachments/9470379/9863813.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_clustal\_omega\_version.xsl](attachments/9470379/9863814.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/9470379/9863815.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/9470379/9863816.xml)
+(application/octet-stream)
+
+Document generated by Confluence on Oct 24, 2018 14:50
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/bioinformatics_tools/alignment_tools/tophat_tophat2.md b/content/guides/running_applications/bioinformatics_tools/alignment_tools/tophat_tophat2.md
new file mode 100644
index 00000000..a2cb83d2
--- /dev/null
+++ b/content/guides/running_applications/bioinformatics_tools/alignment_tools/tophat_tophat2.md
@@ -0,0 +1,1017 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Running Applications](Running-Applications_7471153.html)
+5. [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
+6. [Alignment Tools](Alignment-Tools_8193288.html)
+
+<span id="title-text"> HCC-DOCS : TopHat/TopHat2 </span>
+========================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified by
+<span class="editor"> Natasha Pavlovikj</span> on Sep 07, 2018
+
+| Name | Version | Resource |
+|--------|---------|----------|
+| tophat | 2.0.14 | Tusker |
+| tophat | 2.1.1 | Tusker |
+
+| | | |
+|--------|-------|-------|
+| tophat | 2.0 | Crane |
+| tophat | 2.1.0 | Crane |
+
+
+
+TopHat
+(<a href="http://ccb.jhu.edu/software/tophat/index.shtml" class="external-link">http://ccb.jhu.edu/software/tophat/index.shtml</a>)
+is a fast splice junction mapper for RNA-Seq data. It first aligns
+RNA-Seq reads to reference genomes using the ultra high-throughput short
+read aligner Bowtie, and then analyzes the mapping results to identify
+splice junctions between exons. Although there is no difference between
+the available options for both TopHat and TopHat2 and the number of
+output files, TopHat2 incorporates many significant improvements to
+TopHat. The TopHat package at HCC supports both **tophat** and
+**tophat2**.
+
+The basic usage of TopHat2 is:
+
+**General TopHat2 Usage**
+
+``` syntaxhighlighter-pre
+[tophat|tophat2] [options] index_prefix [input_reads_pair_1.[fasta|fastq] input_reads_pair_2.[fasta|fastq] | input_reads.[fasta|fastq]]
+```
+
+where **index\_prefix** is the basename of the genome index to be
+searched. This index is generated prior running TopHat/TopHat2 by using
+[Bowtie](Bowtie_8193293.html)/[Bowtie2](Bowtie2_8193294.html). TopHat2
+uses single or comma-separated list of paired-end and single-end reads
+in fasta or fastq format. The single-end reads need to be provided after
+the paired-end reads. More advanced TopHat2 options can be found in the
+manual: <a href="http://ccb.jhu.edu/software/tophat/manual.shtml" class="external-link">http://ccb.jhu.edu/software/tophat/manual.shtml</a>,
+or by typing:
+
+**Additional TopHat2 Options**
+
+``` syntaxhighlighter-pre
+[<username>@login.tusker ~]$ tophat2 -h
+```
+
+Prior running TopHat/TopHat2, an index from the reference genome should
+be built using Bowtie/Bowtie2. Moreover, TopHat2 requires both, the
+index file and the reference file, to be in the same directory. If the
+reference file is not available,TopHat2 reconstructs it in its initial
+step using the index file.
+
+An example of how to run TopHat2 on Tusker with paired-end fastq files
+**input\_reads\_pair\_1.fastq** and **input\_reads\_pair\_2.fastq**,
+reference index **index\_prefix** and 8 CPUs is shown below:
+
+**tophat2\_alignment.submit**
+
+\#!/bin/sh
+\#SBATCH --job-name=Tophat2
+\#SBATCH --nodes=1
+\#SBATCH --ntasks-per-node=8
+\#SBATCH --time=168:00:00
+\#SBATCH --mem=50gb
+\#SBATCH --output=Tophat2.%J.out
+\#SBATCH --error=Tophat2.%J.err
+
+
+
+| |
+|------------------------------------------------|
+| module load samtools/1.3 bowtie/2.3 tophat/2.0 |
+
+tophat2 -p $SLURM\_NTASKS\_PER\_NODE index\_prefix
+input\_reads\_pair\_1.fastq input\_reads\_pair\_2.fastq
+
+TopHat2 generates its own output directory *tophat\_output/* that
+contains multiple TopHat2 generated files.
+
+**
+**
+
+**TopHat2 Output**
+
+TopHat2 produces number of files in its *tophat\_out/* output directory.
+Some of the generated files are:
+
+- **accepted\_hits.bam**: list of read alignments in BAM format
+- **unmapped.bam**: list of unmapped reads in BAM format
+- **junctions.bed**: BED track of reported junctions**
+ **
+- **insertions.bed**: BED track of insertions reported by TopHat
+- **deletions.bed**: BED track of deletions reported by TopHat
+- **prep\_reads.info**: statistis about the input sequencing data
+ (min/max read length, number of reads)
+- **align\_summary.txt**: summary of the alignment counts (number of
+ mapped reads, overall read mapping rate)
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/8127568.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_tophat2\_version.xsl](attachments/8193297/8127569.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/8127570.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_tophat2\_version.xsl](attachments/8193297/8127571.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[cb\_tophat2\_module.xsl](attachments/8193297/9863623.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/17044387.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/17044423.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/17044491.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/17044527.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/17044587.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/17044623.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/17044684.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/17044720.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/17044784.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/17044820.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/17044937.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/17044973.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/17047006.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/17047042.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/18546782.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/18546712.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/18546855.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/18546917.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/18547020.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/18546988.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/18547224.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/18547093.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/18547162.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/18547347.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/18547276.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/18547413.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/18547493.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/18547458.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/18547559.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/18547594.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/18547659.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/18547694.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/18547769.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/18547804.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/18547930.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/18547865.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/18547965.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/18548030.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/18548129.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/18548094.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/18548213.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/18548248.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/18548313.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/18548349.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/18548459.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/18548494.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/18548659.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/18548581.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/18548694.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/18548759.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/18548794.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/18548919.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/18548854.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/18548995.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/18548960.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/18549079.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/20709466.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/20709428.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/20709532.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/20709568.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/21069844.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/21069883.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/21069962.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/21070001.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/21070100.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/21070139.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/21070212.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/21070251.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/21070341.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/21070489.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/21070409.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/21070450.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/21070553.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/21070592.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/21070672.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/21070711.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/21070773.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/21070812.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/21070922.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/21071006.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/21070967.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/21071078.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/21071117.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/21071189.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/21071298.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/21071259.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/21071360.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/21071399.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/21071522.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/21071561.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/21071657.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/21071697.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/21071761.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/21071800.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/21071864.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/21071903.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/21071964.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/21072003.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/21072064.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/21072144.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/21072105.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/21072205.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/21072244.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/21072307.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/21072346.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/21072427.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/21072466.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/21072530.xml) (text/xml)
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/35324435.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/35324629.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/35324565.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/35324855.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/35324919.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/35325020.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/35325651.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/35325189.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/35325232.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/35325275.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/35325582.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193297/35325454.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/35325671.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/35325606.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193297/35325480.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193297/35325499.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193297/35325532.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193297/35325869.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/35325699.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/35325723.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/35325764.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/35325784.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/35326160.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/35326184.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/35326751.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/35326771.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193297/35325888.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193297/35325916.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193297/35325935.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193297/35325966.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193297/35326024.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193297/35326095.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193297/35326208.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/35326686.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/35326710.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193297/35326310.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193297/35326404.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193297/35326432.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193297/35326500.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193297/35326550.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193297/35326589.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193297/35326640.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193297/35326662.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193297/35326820.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/17044372.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193297/35325373.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/17044373.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193297/35325372.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193297/35326897.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193297/35326932.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193297/35326951.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193297/35327033.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193297/35325369.xml) (text/xml)
+
+Document generated by Confluence on Oct 24, 2018 14:50
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/bioinformatics_tools/biodata_module/_index.md b/content/guides/running_applications/bioinformatics_tools/biodata_module/_index.md
new file mode 100644
index 00000000..430f5abb
--- /dev/null
+++ b/content/guides/running_applications/bioinformatics_tools/biodata_module/_index.md
@@ -0,0 +1,151 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Running Applications](Running-Applications_7471153.html)
+5. [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
+
+<span id="title-text"> HCC-DOCS : Biodata Module </span>
+========================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified on
+Feb 22, 2017
+
+| Name | Version | Resource |
+|---------|---------|----------|
+| biodata | 1.0 | Tusker |
+
+| Name | Version | Resource |
+|---------|---------|----------|
+| biodata | 1.0 | Crane |
+
+
+HCC hosts multiple databases (BLAST, KEGG, PANTHER, InterProScan),
+genome files, short read aligned indices etc. on both Tusker and
+Crane.
+In order to use these resources, the "**biodata**" module needs to be
+loaded first.
+For how to load module, please check [Module
+Commands](Module-Commands_332464.html).
+
+Loading the "**biodata**" module will pre-set many environment
+variables, but most likely you will only need a subset of them.
+Environment variables can be used in your command or script by prefixing
+a **$** sign to the name.
+
+The major environment variables are:
+**$DATA** - main directory
+**$BLAST** - Directory containing all available BLAST (nucleotide and
+protein) databases
+**$KEGG** - KEGG database main entry point (requires license)
+**$PANTHER** - PANTHER database main entry point (latest)
+**$IPR** - InterProScan database main entry point (latest)
+**$GENOMES** - Directory containing all available genomes (multiple
+sources, builds possible
+**$INDICES** - Directory containing indices for bowtie, bowtie2, bwa for
+all available genomes
+**$UNIPROT** - Directory containing latest release of full UniProt
+database
+
+
+In order to check what genomes are available, you can just type:
+
+**Check available GENOMES**
+
+``` syntaxhighlighter-pre
+ls $GENOMES
+```
+
+
+In order to check what BLAST databases are available, you can just type:
+
+**Check available BLAST databases**
+
+``` syntaxhighlighter-pre
+ls $BLAST
+```
+
+
+An example of how to run Bowtie2 local alignment on Tusker utilizing the
+default Horse, *Equus caballus* index (*BOWTIE2\_HORSE*) with paired-end
+fasta files and 8 CPUs is shown below:
+
+**bowtie2\_alignment.submit**
+
+\#!/bin/sh
+\#SBATCH --job-name=Bowtie2
+\#SBATCH --nodes=1
+\#SBATCH --ntasks-per-node=8
+\#SBATCH --time=168:00:00
+\#SBATCH --mem=50gb
+\#SBATCH --output=Bowtie2.%J.out
+\#SBATCH --error=Bowtie2.%J.err
+
+
+
+module load biodata/1.0
+
+module load bowtie/2.2
+
+bowtie2 -x $BOWTIE2\_HORSE -f -1 input\_reads\_pair\_1.fasta -2
+input\_reads\_pair\_2.fasta -S bowtie2\_alignments.sam --local -p
+$SLURM\_NTASKS\_PER\_NODE
+
+
+An example of BLAST run against the yeast nucleotide database available
+on Tusker is provided below:
+
+**blastn\_alignment.submit**
+
+\#!/bin/sh
+\#SBATCH --job-name=BlastN
+\#SBATCH --nodes=1
+\#SBATCH --ntasks-per-node=8
+\#SBATCH --time=168:00:00
+\#SBATCH --mem=50gb
+\#SBATCH --output=BlastN.%J.out
+\#SBATCH --error=BlastN.%J.err
+
+
+
+module load biodata/1.0
+
+module load blast/2.2
+
+cp $BLAST/yeast.nt.\* /tmp
+cp yeast.query /tmp
+
+blastn -db /tmp/yeast.nt -query /tmp/yeast.query -out
+/tmp/blast\_nucleotide.results
+
+cp /tmp/blast\_nucleotide.results .
+
+
+The organisms and their appropriate environmental variables for all
+genomes and chromosome files, as well as for short read aligned indices
+are shown on the link below:
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[cb\_blastn\_biodata.xsl](attachments/15171887/15171888.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[cb\_bowtie2\_biodata.xsl](attachments/15171887/15171889.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_biodata\_version.xsl](attachments/15171887/15171890.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/15171887/15171891.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_biodata\_version.xsl](attachments/15171887/15171892.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/15171887/15171893.xml)
+(application/octet-stream)
+
+Document generated by Confluence on Oct 24, 2018 14:54
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/bioinformatics_tools/biodata_module/organisms.md b/content/guides/running_applications/bioinformatics_tools/biodata_module/organisms.md
new file mode 100644
index 00000000..4643debc
--- /dev/null
+++ b/content/guides/running_applications/bioinformatics_tools/biodata_module/organisms.md
@@ -0,0 +1,786 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Running Applications](Running-Applications_7471153.html)
+5. [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
+6. [Biodata Module](Biodata-Module_15171887.html)
+
+<span id="title-text"> HCC-DOCS : Organisms </span>
+===================================================
+
+Created by <span class="author"> Adam Caprez</span> on Mar 10, 2016
+
+<span
+class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
+class="expand-control-text">Arabidopsis\_thaliana</span>
+
+| Short Name | Source | Build | Type |
+|----------------------------------------------|--------|--------|----------------------------|
+| ARABIDOPSIS\_THALIANA\_NCBI\_TAIR10 | NCBI | TAIR10 | Main Directory |
+| ATH | NCBI | TAIR10 | Main Directory |
+| BOWTIE\_ARABIDOPSIS\_THALIANA\_NCBI\_TAIR10 | NCBI | TAIR10 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE\_ATH | NCBI | TAIR10 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_ARABIDOPSIS\_THALIANA\_NCBI\_TAIR10 | NCBI | TAIR10 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_ATH | NCBI | TAIR10 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_ARABIDOPSIS\_THALIANA\_NCBI\_TAIR10 | NCBI | TAIR10 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_ATH | NCBI | TAIR10 | Bwa\|Bowtie\|Bowtie2 Index |
+| CHR\_ARABIDOPSIS\_THALIANA\_NCBI\_TAIR10 | NCBI | TAIR10 | Chromosome Fasta Files |
+| CHR\_ATH | NCBI | TAIR10 | Chromosome Fasta Files |
+| FAIDX\_ARABIDOPSIS\_THALIANA\_NCBI\_TAIR10 | NCBI | TAIR10 | Fasta Index .fai File |
+| FAIDX\_ATH | NCBI | TAIR10 | Fasta Index .fai File |
+| GENOME\_ARABIDOPSIS\_THALIANA\_NCBI\_TAIR10 | NCBI | TAIR10 | Genome Fasta File |
+| GENOME\_ATH | NCBI | TAIR10 | Genome Fasta File |
+| PICARD\_ARABIDOPSIS\_THALIANA\_NCBI\_TAIR10 | NCBI | TAIR10 | Picard .dict File |
+| PICARD\_ATH | NCBI | TAIR10 | Picard .dict File |
+
+<span
+class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
+class="expand-control-text">Bacillus\_cereus\_ATCC\_10987</span>
+
+| Short Name | Source | Build | Type |
+|------------------------------------------------------------|--------|------------|----------------------------|
+| BACILLUS\_CEREUS\_ATCC\_10987 | NCBI | 2004-02-13 | Main Directory |
+| BACILLUS\_CEREUS\_ATCC\_10987\_NCBI\_2004\_02\_13 | NCBI | 2004-02-13 | Main Directory |
+| BOWTIE\_BACILLUS\_CEREUS\_ATCC\_10987 | NCBI | 2004-02-13 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE\_BACILLUS\_CEREUS\_ATCC\_10987\_NCBI\_2004\_02\_13 | NCBI | 2004-02-13 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_BACILLUS\_CEREUS\_ATCC\_10987 | NCBI | 2004-02-13 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_BACILLUS\_CEREUS\_ATCC\_10987\_NCBI\_2004\_02\_13 | NCBI | 2004-02-13 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_BACILLUS\_CEREUS\_ATCC\_10987 | NCBI | 2004-02-13 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_BACILLUS\_CEREUS\_ATCC\_10987\_NCBI\_2004\_02\_13 | NCBI | 2004-02-13 | Bwa\|Bowtie\|Bowtie2 Index |
+| CHR\_BACILLUS\_CEREUS\_ATCC\_10987 | NCBI | 2004-02-13 | Chromosome Fasta Files |
+| CHR\_BACILLUS\_CEREUS\_ATCC\_10987\_NCBI\_2004\_02\_13 | NCBI | 2004-02-13 | Chromosome Fasta Files |
+| FAIDX\_BACILLUS\_CEREUS\_ATCC\_10987 | NCBI | 2004-02-13 | Fasta Index .fai File |
+| FAIDX\_BACILLUS\_CEREUS\_ATCC\_10987\_NCBI\_2004\_02\_13 | NCBI | 2004-02-13 | Fasta Index .fai File |
+| GENOME\_BACILLUS\_CEREUS\_ATCC\_10987 | NCBI | 2004-02-13 | Genome Fasta File |
+| GENOME\_BACILLUS\_CEREUS\_ATCC\_10987\_NCBI\_2004\_02\_13 | NCBI | 2004-02-13 | Genome Fasta File |
+| PICARD\_BACILLUS\_CEREUS\_ATCC\_10987 | NCBI | 2004-02-13 | Picard .dict File |
+| PICARD\_BACILLUS\_CEREUS\_ATCC\_10987\_NCBI\_2004\_02\_13 | NCBI | 2004-02-13 | Picard .dict File |
+
+<span
+class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
+class="expand-control-text">Bacillus\_subtilis\_168</span>
+
+| Short Name | Source | Build | Type |
+|------------------------------------------------|---------|-------|----------------------------|
+| BACILLUS\_SUBTILIS\_168\_ENSEMBL\_EB2 | Ensembl | EB2 | Main Directory |
+| BOWTIE\_BACILLUS\_SUBTILIS\_168\_ENSEMBL\_EB2 | Ensembl | EB2 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE\_BSUBT\_168 | Ensembl | EB2 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_BACILLUS\_SUBTILIS\_168\_ENSEMBL\_EB2 | Ensembl | EB2 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_BSUBT\_168 | Ensembl | EB2 | Bwa\|Bowtie\|Bowtie2 Index |
+| BSUBT\_168 | Ensembl | EB2 | Main Directory |
+| BWA\_BACILLUS\_SUBTILIS\_168\_ENSEMBL\_EB2 | Ensembl | EB2 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_BSUBT\_168 | Ensembl | EB2 | Bwa\|Bowtie\|Bowtie2 Index |
+| CHR\_BACILLUS\_SUBTILIS\_168\_ENSEMBL\_EB2 | Ensembl | EB2 | Chromosome Fasta Files |
+| CHR\_BSUBT\_168 | Ensembl | EB2 | Chromosome Fasta Files |
+| FAIDX\_BACILLUS\_SUBTILIS\_168\_ENSEMBL\_EB2 | Ensembl | EB2 | Fasta Index .fai File |
+| FAIDX\_BSUBT\_168 | Ensembl | EB2 | Fasta Index .fai File |
+| GENOME\_BACILLUS\_SUBTILIS\_168\_ENSEMBL\_EB2 | Ensembl | EB2 | Genome Fasta File |
+| GENOME\_BSUBT\_168 | Ensembl | EB2 | Genome Fasta File |
+| PICARD\_BACILLUS\_SUBTILIS\_168\_ENSEMBL\_EB2 | Ensembl | EB2 | Picard .dict File |
+| PICARD\_BSUBT\_168 | Ensembl | EB2 | Picard .dict File |
+
+<span
+class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
+class="expand-control-text">Bos\_taurus</span>
+
+| Short Name | Source | Build | Type |
+|------------------------------------------|---------|------------|----------------------------|
+| BOS\_TAURUS\_ENSEMBL\_UMD\_3\_1 | Ensembl | UMD\_3.1 | Main Directory |
+| BOS\_TAURUS\_ENSEMBL\_UMD3\_1 | Ensembl | UMD3.1 | Main Directory |
+| BOS\_TAURUS\_NCBI\_UMD\_3\_1 | NCBI | UMD\_3.1 | Main Directory |
+| BOS\_TAURUS\_NCBI\_UMD\_3\_1\_1 | NCBI | UMD\_3.1.1 | Main Directory |
+| BOWTIE\_BOS\_TAURUS\_ENSEMBL\_UMD\_3\_1 | Ensembl | UMD\_3.1 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE\_BOS\_TAURUS\_ENSEMBL\_UMD3\_1 | Ensembl | UMD3.1 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE\_BOS\_TAURUS\_NCBI\_UMD\_3\_1 | NCBI | UMD\_3.1 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE\_BOS\_TAURUS\_NCBI\_UMD\_3\_1\_1 | NCBI | UMD\_3.1.1 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE\_COW | NCBI | UMD\_3.1 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_BOS\_TAURUS\_ENSEMBL\_UMD\_3\_1 | Ensembl | UMD\_3.1 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_BOS\_TAURUS\_ENSEMBL\_UMD3\_1 | Ensembl | UMD3.1 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_BOS\_TAURUS\_NCBI\_UMD\_3\_1 | NCBI | UMD\_3.1 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_BOS\_TAURUS\_NCBI\_UMD\_3\_1\_1 | NCBI | UMD\_3.1.1 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_COW | NCBI | UMD\_3.1 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_BOS\_TAURUS\_ENSEMBL\_UMD\_3\_1 | Ensembl | UMD\_3.1 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_BOS\_TAURUS\_ENSEMBL\_UMD3\_1 | Ensembl | UMD3.1 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_BOS\_TAURUS\_NCBI\_UMD\_3\_1 | NCBI | UMD\_3.1 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_BOS\_TAURUS\_NCBI\_UMD\_3\_1\_1 | NCBI | UMD\_3.1.1 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_COW | NCBI | UMD\_3.1 | Bwa\|Bowtie\|Bowtie2 Index |
+| CHR\_BOS\_TAURUS\_ENSEMBL\_UMD\_3\_1 | Ensembl | UMD\_3.1 | Chromosome Fasta Files |
+| CHR\_BOS\_TAURUS\_ENSEMBL\_UMD3\_1 | Ensembl | UMD3.1 | Chromosome Fasta Files |
+| CHR\_BOS\_TAURUS\_NCBI\_UMD\_3\_1 | NCBI | UMD\_3.1 | Chromosome Fasta Files |
+| CHR\_BOS\_TAURUS\_NCBI\_UMD\_3\_1\_1 | NCBI | UMD\_3.1.1 | Chromosome Fasta Files |
+| CHR\_COW | NCBI | UMD\_3.1 | Chromosome Fasta Files |
+| COW | NCBI | UMD\_3.1 | Main Directory |
+| FAIDX\_BOS\_TAURUS\_ENSEMBL\_UMD\_3\_1 | Ensembl | UMD\_3.1 | Fasta Index .fai File |
+| FAIDX\_BOS\_TAURUS\_ENSEMBL\_UMD3\_1 | Ensembl | UMD3.1 | Fasta Index .fai File |
+| FAIDX\_BOS\_TAURUS\_NCBI\_UMD\_3\_1 | NCBI | UMD\_3.1 | Fasta Index .fai File |
+| FAIDX\_BOS\_TAURUS\_NCBI\_UMD\_3\_1\_1 | NCBI | UMD\_3.1.1 | Fasta Index .fai File |
+| FAIDX\_COW | NCBI | UMD\_3.1 | Fasta Index .fai File |
+| GENOME\_BOS\_TAURUS\_ENSEMBL\_UMD\_3\_1 | Ensembl | UMD\_3.1 | Genome Fasta File |
+| GENOME\_BOS\_TAURUS\_ENSEMBL\_UMD3\_1 | Ensembl | UMD3.1 | Genome Fasta File |
+| GENOME\_BOS\_TAURUS\_NCBI\_UMD\_3\_1 | NCBI | UMD\_3.1 | Genome Fasta File |
+| GENOME\_BOS\_TAURUS\_NCBI\_UMD\_3\_1\_1 | NCBI | UMD\_3.1.1 | Genome Fasta File |
+| GENOME\_COW | NCBI | UMD\_3.1 | Genome Fasta File |
+| PICARD\_BOS\_TAURUS\_ENSEMBL\_UMD\_3\_1 | Ensembl | UMD\_3.1 | Picard .dict File |
+| PICARD\_BOS\_TAURUS\_ENSEMBL\_UMD3\_1 | Ensembl | UMD3.1 | Picard .dict File |
+| PICARD\_BOS\_TAURUS\_NCBI\_UMD\_3\_1 | NCBI | UMD\_3.1 | Picard .dict File |
+| PICARD\_BOS\_TAURUS\_NCBI\_UMD\_3\_1\_1 | NCBI | UMD\_3.1.1 | Picard .dict File |
+| PICARD\_COW | NCBI | UMD\_3.1 | Picard .dict File |
+
+<span
+class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
+class="expand-control-text">Caenorhabditis\_elegans</span>
+
+| Short Name | Source | Build | Type |
+|-----------------------------------------------|--------|-------|----------------------------|
+| BOWTIE\_CAENORHABDITIS\_ELEGANS\_NCBI\_WS195 | NCBI | WS195 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE\_CELEGANS | NCBI | WS195 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_CAENORHABDITIS\_ELEGANS\_NCBI\_WS195 | NCBI | WS195 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_CELEGANS | NCBI | WS195 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_CAENORHABDITIS\_ELEGANS\_NCBI\_WS195 | NCBI | WS195 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_CELEGANS | NCBI | WS195 | Bwa\|Bowtie\|Bowtie2 Index |
+| CAENORHABDITIS\_ELEGANS\_NCBI\_WS195 | NCBI | WS195 | Main Directory |
+| CELEGANS | NCBI | WS195 | Main Directory |
+| CHR\_CAENORHABDITIS\_ELEGANS\_NCBI\_WS195 | NCBI | WS195 | Chromosome Fasta Files |
+| CHR\_CELEGANS | NCBI | WS195 | Chromosome Fasta Files |
+| FAIDX\_CAENORHABDITIS\_ELEGANS\_NCBI\_WS195 | NCBI | WS195 | Fasta Index .fai File |
+| FAIDX\_CELEGANS | NCBI | WS195 | Fasta Index .fai File |
+| GENOME\_CAENORHABDITIS\_ELEGANS\_NCBI\_WS195 | NCBI | WS195 | Genome Fasta File |
+| GENOME\_CELEGANS | NCBI | WS195 | Genome Fasta File |
+| PICARD\_CAENORHABDITIS\_ELEGANS\_NCBI\_WS195 | NCBI | WS195 | Picard .dict File |
+| PICARD\_CELEGANS | NCBI | WS195 | Picard .dict File |
+
+<span
+class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
+class="expand-control-text">Canis\_familiaris</span>
+
+| Short Name | Source | Build | Type |
+|---------------------------------------------|--------|----------|----------------------------|
+| BOWTIE\_CANIS\_FAMILIARIS\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE\_DOG | NCBI | build3.1 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_CANIS\_FAMILIARIS\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_DOG | NCBI | build3.1 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_CANIS\_FAMILIARIS\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_DOG | NCBI | build3.1 | Bwa\|Bowtie\|Bowtie2 Index |
+| CANIS\_FAMILIARIS\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Main Directory |
+| CHR\_CANIS\_FAMILIARIS\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Chromosome Fasta Files |
+| CHR\_DOG | NCBI | build3.1 | Chromosome Fasta Files |
+| DOG | NCBI | build3.1 | Main Directory |
+| FAIDX\_CANIS\_FAMILIARIS\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Fasta Index .fai File |
+| FAIDX\_DOG | NCBI | build3.1 | Fasta Index .fai File |
+| GENOME\_CANIS\_FAMILIARIS\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Genome Fasta File |
+| GENOME\_DOG | NCBI | build3.1 | Genome Fasta File |
+| PICARD\_CANIS\_FAMILIARIS\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Picard .dict File |
+| PICARD\_DOG | NCBI | build3.1 | Picard .dict File |
+
+<span
+class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
+class="expand-control-text">Danio\_rerio</span>
+
+| Short Name | Source | Build | Type |
+|----------------------------------|--------|-------|----------------------------|
+| BOWTIE\_DANIO\_RERIO | NCBI | Zv9 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE\_DANIO\_RERIO\_NCBI\_ZV9 | NCBI | Zv9 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_DANIO\_RERIO | NCBI | Zv9 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_DANIO\_RERIO\_NCBI\_ZV9 | NCBI | Zv9 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_DANIO\_RERIO | NCBI | Zv9 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_DANIO\_RERIO\_NCBI\_ZV9 | NCBI | Zv9 | Bwa\|Bowtie\|Bowtie2 Index |
+| CHR\_DANIO\_RERIO | NCBI | Zv9 | Chromosome Fasta Files |
+| CHR\_DANIO\_RERIO\_NCBI\_ZV9 | NCBI | Zv9 | Chromosome Fasta Files |
+| DANIO\_RERIO | NCBI | Zv9 | Main Directory |
+| DANIO\_RERIO\_NCBI\_ZV9 | NCBI | Zv9 | Main Directory |
+| FAIDX\_DANIO\_RERIO | NCBI | Zv9 | Fasta Index .fai File |
+| FAIDX\_DANIO\_RERIO\_NCBI\_ZV9 | NCBI | Zv9 | Fasta Index .fai File |
+| GENOME\_DANIO\_RERIO | NCBI | Zv9 | Genome Fasta File |
+| GENOME\_DANIO\_RERIO\_NCBI\_ZV9 | NCBI | Zv9 | Genome Fasta File |
+| PICARD\_DANIO\_RERIO | NCBI | Zv9 | Picard .dict File |
+| PICARD\_DANIO\_RERIO\_NCBI\_ZV9 | NCBI | Zv9 | Picard .dict File |
+
+<span
+class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
+class="expand-control-text">Drosophila\_melanogaster</span>
+
+| Short Name | Source | Build | Type |
+|-----------------------------------------------------|--------|-----------|----------------------------|
+| BOWTIE\_DROSOPHILA\_MELANOGASTER | NCBI | build5.41 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE\_DROSOPHILA\_MELANOGASTER\_NCBI\_BUILD5\_41 | NCBI | build5.41 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_DROSOPHILA\_MELANOGASTER | NCBI | build5.41 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_DROSOPHILA\_MELANOGASTER\_NCBI\_BUILD5\_41 | NCBI | build5.41 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_DROSOPHILA\_MELANOGASTER | NCBI | build5.41 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_DROSOPHILA\_MELANOGASTER\_NCBI\_BUILD5\_41 | NCBI | build5.41 | Bwa\|Bowtie\|Bowtie2 Index |
+| CHR\_DROSOPHILA\_MELANOGASTER | NCBI | build5.41 | Chromosome Fasta Files |
+| CHR\_DROSOPHILA\_MELANOGASTER\_NCBI\_BUILD5\_41 | NCBI | build5.41 | Chromosome Fasta Files |
+| DROSOPHILA\_MELANOGASTER | NCBI | build5.41 | Main Directory |
+| DROSOPHILA\_MELANOGASTER\_NCBI\_BUILD5\_41 | NCBI | build5.41 | Main Directory |
+| FAIDX\_DROSOPHILA\_MELANOGASTER | NCBI | build5.41 | Fasta Index .fai File |
+| FAIDX\_DROSOPHILA\_MELANOGASTER\_NCBI\_BUILD5\_41 | NCBI | build5.41 | Fasta Index .fai File |
+| GENOME\_DROSOPHILA\_MELANOGASTER | NCBI | build5.41 | Genome Fasta File |
+| GENOME\_DROSOPHILA\_MELANOGASTER\_NCBI\_BUILD5\_41 | NCBI | build5.41 | Genome Fasta File |
+| PICARD\_DROSOPHILA\_MELANOGASTER | NCBI | build5.41 | Picard .dict File |
+| PICARD\_DROSOPHILA\_MELANOGASTER\_NCBI\_BUILD5\_41 | NCBI | build5.41 | Picard .dict File |
+
+<span
+class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
+class="expand-control-text">Enterobacteriophage\_lambda</span>
+
+| Short Name | Source | Build | Type |
+|----------------------------------------------------------|--------|------------|----------------------------|
+| BOWTIE\_ELAMBDA | NCBI | 1993-04-28 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE\_ENTEROBACTERIOPHAGE\_LAMBDA\_NCBI\_1993\_04\_28 | NCBI | 1993-04-28 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_ELAMBDA | NCBI | 1993-04-28 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_ENTEROBACTERIOPHAGE\_LAMBDA\_NCBI\_1993\_04\_28 | NCBI | 1993-04-28 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_ELAMBDA | NCBI | 1993-04-28 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_ENTEROBACTERIOPHAGE\_LAMBDA\_NCBI\_1993\_04\_28 | NCBI | 1993-04-28 | Bwa\|Bowtie\|Bowtie2 Index |
+| CHR\_ELAMBDA | NCBI | 1993-04-28 | Chromosome Fasta Files |
+| CHR\_ENTEROBACTERIOPHAGE\_LAMBDA\_NCBI\_1993\_04\_28 | NCBI | 1993-04-28 | Chromosome Fasta Files |
+| ELAMBDA | NCBI | 1993-04-28 | Main Directory |
+| ENTEROBACTERIOPHAGE\_LAMBDA\_NCBI\_1993\_04\_28 | NCBI | 1993-04-28 | Main Directory |
+| FAIDX\_ELAMBDA | NCBI | 1993-04-28 | Fasta Index .fai File |
+| FAIDX\_ENTEROBACTERIOPHAGE\_LAMBDA\_NCBI\_1993\_04\_28 | NCBI | 1993-04-28 | Fasta Index .fai File |
+| GENOME\_ELAMBDA | NCBI | 1993-04-28 | Genome Fasta File |
+| GENOME\_ENTEROBACTERIOPHAGE\_LAMBDA\_NCBI\_1993\_04\_28 | NCBI | 1993-04-28 | Genome Fasta File |
+| PICARD\_ELAMBDA | NCBI | 1993-04-28 | Picard .dict File |
+| PICARD\_ENTEROBACTERIOPHAGE\_LAMBDA\_NCBI\_1993\_04\_28 | NCBI | 1993-04-28 | Picard .dict File |
+
+<span
+class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
+class="expand-control-text">Equus\_caballus</span>
+
+| Short Name | Source | Build | Type |
+|--------------------------------------------|--------|-----------|----------------------------|
+| BOWTIE\_EQUUS\_CABALLUS\_NCBI\_EQUCAB2\_0 | NCBI | EquCab2.0 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE\_HORSE | NCBI | EquCab2.0 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_EQUUS\_CABALLUS\_NCBI\_EQUCAB2\_0 | NCBI | EquCab2.0 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_HORSE | NCBI | EquCab2.0 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_EQUUS\_CABALLUS\_NCBI\_EQUCAB2\_0 | NCBI | EquCab2.0 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_HORSE | NCBI | EquCab2.0 | Bwa\|Bowtie\|Bowtie2 Index |
+| CHR\_EQUUS\_CABALLUS\_NCBI\_EQUCAB2\_0 | NCBI | EquCab2.0 | Chromosome Fasta Files |
+| CHR\_HORSE | NCBI | EquCab2.0 | Chromosome Fasta Files |
+| EQUUS\_CABALLUS\_NCBI\_EQUCAB2\_0 | NCBI | EquCab2.0 | Main Directory |
+| FAIDX\_EQUUS\_CABALLUS\_NCBI\_EQUCAB2\_0 | NCBI | EquCab2.0 | Fasta Index .fai File |
+| FAIDX\_HORSE | NCBI | EquCab2.0 | Fasta Index .fai File |
+| GENOME\_EQUUS\_CABALLUS\_NCBI\_EQUCAB2\_0 | NCBI | EquCab2.0 | Genome Fasta File |
+| GENOME\_HORSE | NCBI | EquCab2.0 | Genome Fasta File |
+| HORSE | NCBI | EquCab2.0 | Main Directory |
+| PICARD\_EQUUS\_CABALLUS\_NCBI\_EQUCAB2\_0 | NCBI | EquCab2.0 | Picard .dict File |
+| PICARD\_HORSE | NCBI | EquCab2.0 | Picard .dict File |
+
+<span
+class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
+class="expand-control-text">Escherichia\_coli\_K\_12\_DH10B</span>
+
+| Short Name | Source | Build | Type |
+|--------------------------------------------------------------|--------|------------|----------------------------|
+| BOWTIE\_ESCHERICHIA\_COLI\_K\_12\_DH10B | NCBI | 2008-03-17 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE\_ESCHERICHIA\_COLI\_K\_12\_DH10B\_NCBI\_2008\_03\_17 | NCBI | 2008-03-17 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_ESCHERICHIA\_COLI\_K\_12\_DH10B | NCBI | 2008-03-17 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_ESCHERICHIA\_COLI\_K\_12\_DH10B\_NCBI\_2008\_03\_17 | NCBI | 2008-03-17 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_ESCHERICHIA\_COLI\_K\_12\_DH10B | NCBI | 2008-03-17 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_ESCHERICHIA\_COLI\_K\_12\_DH10B\_NCBI\_2008\_03\_17 | NCBI | 2008-03-17 | Bwa\|Bowtie\|Bowtie2 Index |
+| CHR\_ESCHERICHIA\_COLI\_K\_12\_DH10B | NCBI | 2008-03-17 | Chromosome Fasta Files |
+| CHR\_ESCHERICHIA\_COLI\_K\_12\_DH10B\_NCBI\_2008\_03\_17 | NCBI | 2008-03-17 | Chromosome Fasta Files |
+| ESCHERICHIA\_COLI\_K\_12\_DH10B | NCBI | 2008-03-17 | Main Directory |
+| ESCHERICHIA\_COLI\_K\_12\_DH10B\_NCBI\_2008\_03\_17 | NCBI | 2008-03-17 | Main Directory |
+| FAIDX\_ESCHERICHIA\_COLI\_K\_12\_DH10B | NCBI | 2008-03-17 | Fasta Index .fai File |
+| FAIDX\_ESCHERICHIA\_COLI\_K\_12\_DH10B\_NCBI\_2008\_03\_17 | NCBI | 2008-03-17 | Fasta Index .fai File |
+| GENOME\_ESCHERICHIA\_COLI\_K\_12\_DH10B | NCBI | 2008-03-17 | Genome Fasta File |
+| GENOME\_ESCHERICHIA\_COLI\_K\_12\_DH10B\_NCBI\_2008\_03\_17 | NCBI | 2008-03-17 | Genome Fasta File |
+| PICARD\_ESCHERICHIA\_COLI\_K\_12\_DH10B | NCBI | 2008-03-17 | Picard .dict File |
+| PICARD\_ESCHERICHIA\_COLI\_K\_12\_DH10B\_NCBI\_2008\_03\_17 | NCBI | 2008-03-17 | Picard .dict File |
+
+<span
+class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
+class="expand-control-text">Escherichia\_coli\_K\_12\_MG1655</span>
+
+| Short Name | Source | Build | Type |
+|---------------------------------------------------------------|--------|------------|----------------------------|
+| BOWTIE\_ESCHERICHIA\_COLI\_K\_12\_MG1655 | NCBI | 2001-10-15 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE\_ESCHERICHIA\_COLI\_K\_12\_MG1655\_NCBI\_2001\_10\_15 | NCBI | 2001-10-15 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_ESCHERICHIA\_COLI\_K\_12\_MG1655 | NCBI | 2001-10-15 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_ESCHERICHIA\_COLI\_K\_12\_MG1655\_NCBI\_2001\_10\_15 | NCBI | 2001-10-15 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_ESCHERICHIA\_COLI\_K\_12\_MG1655 | NCBI | 2001-10-15 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_ESCHERICHIA\_COLI\_K\_12\_MG1655\_NCBI\_2001\_10\_15 | NCBI | 2001-10-15 | Bwa\|Bowtie\|Bowtie2 Index |
+| CHR\_ESCHERICHIA\_COLI\_K\_12\_MG1655 | NCBI | 2001-10-15 | Chromosome Fasta Files |
+| CHR\_ESCHERICHIA\_COLI\_K\_12\_MG1655\_NCBI\_2001\_10\_15 | NCBI | 2001-10-15 | Chromosome Fasta Files |
+| ESCHERICHIA\_COLI\_K\_12\_MG1655 | NCBI | 2001-10-15 | Main Directory |
+| ESCHERICHIA\_COLI\_K\_12\_MG1655\_NCBI\_2001\_10\_15 | NCBI | 2001-10-15 | Main Directory |
+| FAIDX\_ESCHERICHIA\_COLI\_K\_12\_MG1655 | NCBI | 2001-10-15 | Fasta Index .fai File |
+| FAIDX\_ESCHERICHIA\_COLI\_K\_12\_MG1655\_NCBI\_2001\_10\_15 | NCBI | 2001-10-15 | Fasta Index .fai File |
+| GENOME\_ESCHERICHIA\_COLI\_K\_12\_MG1655 | NCBI | 2001-10-15 | Genome Fasta File |
+| GENOME\_ESCHERICHIA\_COLI\_K\_12\_MG1655\_NCBI\_2001\_10\_15 | NCBI | 2001-10-15 | Genome Fasta File |
+| PICARD\_ESCHERICHIA\_COLI\_K\_12\_MG1655 | NCBI | 2001-10-15 | Picard .dict File |
+| PICARD\_ESCHERICHIA\_COLI\_K\_12\_MG1655\_NCBI\_2001\_10\_15 | NCBI | 2001-10-15 | Picard .dict File |
+
+<span
+class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
+class="expand-control-text">Gallus\_gallus</span>
+
+| Short Name | Source | Build | Type |
+|------------------------------------------|--------|----------|----------------------------|
+| BOWTIE\_GALLUS\_GALLUS | NCBI | build3.1 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE\_GALLUS\_GALLUS\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_GALLUS\_GALLUS | NCBI | build3.1 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_GALLUS\_GALLUS\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_GALLUS\_GALLUS | NCBI | build3.1 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_GALLUS\_GALLUS\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Bwa\|Bowtie\|Bowtie2 Index |
+| CHR\_GALLUS\_GALLUS | NCBI | build3.1 | Chromosome Fasta Files |
+| CHR\_GALLUS\_GALLUS\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Chromosome Fasta Files |
+| FAIDX\_GALLUS\_GALLUS | NCBI | build3.1 | Fasta Index .fai File |
+| FAIDX\_GALLUS\_GALLUS\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Fasta Index .fai File |
+| GALLUS\_GALLUS | NCBI | build3.1 | Main Directory |
+| GALLUS\_GALLUS\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Main Directory |
+| GENOME\_GALLUS\_GALLUS | NCBI | build3.1 | Genome Fasta File |
+| GENOME\_GALLUS\_GALLUS\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Genome Fasta File |
+| PICARD\_GALLUS\_GALLUS | NCBI | build3.1 | Picard .dict File |
+| PICARD\_GALLUS\_GALLUS\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Picard .dict File |
+
+<span
+class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
+class="expand-control-text">Glycine\_max</span>
+
+| Short Name | Source | Build | Type |
+|--------------------------------------|---------|-------|----------------------------|
+| BOWTIE\_GLYCINE\_MAX\_ENSEMBL\_GM01 | Ensembl | Gm01 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE\_SOYBEAN | Ensembl | Gm01 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_GLYCINE\_MAX\_ENSEMBL\_GM01 | Ensembl | Gm01 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_SOYBEAN | Ensembl | Gm01 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_GLYCINE\_MAX\_ENSEMBL\_GM01 | Ensembl | Gm01 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_SOYBEAN | Ensembl | Gm01 | Bwa\|Bowtie\|Bowtie2 Index |
+| CHR\_GLYCINE\_MAX\_ENSEMBL\_GM01 | Ensembl | Gm01 | Chromosome Fasta Files |
+| CHR\_SOYBEAN | Ensembl | Gm01 | Chromosome Fasta Files |
+| FAIDX\_GLYCINE\_MAX\_ENSEMBL\_GM01 | Ensembl | Gm01 | Fasta Index .fai File |
+| FAIDX\_SOYBEAN | Ensembl | Gm01 | Fasta Index .fai File |
+| GENOME\_GLYCINE\_MAX\_ENSEMBL\_GM01 | Ensembl | Gm01 | Genome Fasta File |
+| GENOME\_SOYBEAN | Ensembl | Gm01 | Genome Fasta File |
+| GLYCINE\_MAX\_ENSEMBL\_GM01 | Ensembl | Gm01 | Main Directory |
+| PICARD\_GLYCINE\_MAX\_ENSEMBL\_GM01 | Ensembl | Gm01 | Picard .dict File |
+| PICARD\_SOYBEAN | Ensembl | Gm01 | Picard .dict File |
+| SOYBEAN | Ensembl | Gm01 | Main Directory |
+
+<span
+class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
+class="expand-control-text">Homo\_sapiens</span>
+
+| Short Name | Source | Build | Type |
+|------------------------------------------|--------|-----------|----------------------------|
+| BOWTIE\_HOMO\_SAPIENS\_NCBI\_BUILD37\_2 | NCBI | build37.2 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE\_HUMAN | NCBI | build37.2 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_HOMO\_SAPIENS\_NCBI\_BUILD37\_2 | NCBI | build37.2 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_HUMAN | NCBI | build37.2 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_HOMO\_SAPIENS\_NCBI\_BUILD37\_2 | NCBI | build37.2 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_HUMAN | NCBI | build37.2 | Bwa\|Bowtie\|Bowtie2 Index |
+| CHR\_HOMO\_SAPIENS\_NCBI\_BUILD37\_2 | NCBI | build37.2 | Chromosome Fasta Files |
+| CHR\_HUMAN | NCBI | build37.2 | Chromosome Fasta Files |
+| FAIDX\_HOMO\_SAPIENS\_NCBI\_BUILD37\_2 | NCBI | build37.2 | Fasta Index .fai File |
+| FAIDX\_HUMAN | NCBI | build37.2 | Fasta Index .fai File |
+| GENOME\_HOMO\_SAPIENS\_NCBI\_BUILD37\_2 | NCBI | build37.2 | Genome Fasta File |
+| GENOME\_HUMAN | NCBI | build37.2 | Genome Fasta File |
+| HOMO\_SAPIENS\_NCBI\_BUILD37\_2 | NCBI | build37.2 | Main Directory |
+| HUMAN | NCBI | build37.2 | Main Directory |
+| PICARD\_HOMO\_SAPIENS\_NCBI\_BUILD37\_2 | NCBI | build37.2 | Picard .dict File |
+| PICARD\_HUMAN | NCBI | build37.2 | Picard .dict File |
+
+<span
+class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
+class="expand-control-text">Macaca\_mulatta</span>
+
+| Short Name | Source | Build | Type |
+|--------------------------------------------|---------|---------|----------------------------|
+| BOWTIE\_MACACA\_MULATTA | Ensembl | Mmul\_1 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE\_MACACA\_MULATTA\_ENSEMBL\_MMUL\_1 | Ensembl | Mmul\_1 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_MACACA\_MULATTA | Ensembl | Mmul\_1 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_MACACA\_MULATTA\_ENSEMBL\_MMUL\_1 | Ensembl | Mmul\_1 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_MACACA\_MULATTA | Ensembl | Mmul\_1 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_MACACA\_MULATTA\_ENSEMBL\_MMUL\_1 | Ensembl | Mmul\_1 | Bwa\|Bowtie\|Bowtie2 Index |
+| CHR\_MACACA\_MULATTA | Ensembl | Mmul\_1 | Chromosome Fasta Files |
+| CHR\_MACACA\_MULATTA\_ENSEMBL\_MMUL\_1 | Ensembl | Mmul\_1 | Chromosome Fasta Files |
+| FAIDX\_MACACA\_MULATTA | Ensembl | Mmul\_1 | Fasta Index .fai File |
+| FAIDX\_MACACA\_MULATTA\_ENSEMBL\_MMUL\_1 | Ensembl | Mmul\_1 | Fasta Index .fai File |
+| GENOME\_MACACA\_MULATTA | Ensembl | Mmul\_1 | Genome Fasta File |
+| GENOME\_MACACA\_MULATTA\_ENSEMBL\_MMUL\_1 | Ensembl | Mmul\_1 | Genome Fasta File |
+| MACACA\_MULATTA | Ensembl | Mmul\_1 | Main Directory |
+| MACACA\_MULATTA\_ENSEMBL\_MMUL\_1 | Ensembl | Mmul\_1 | Main Directory |
+| PICARD\_MACACA\_MULATTA | Ensembl | Mmul\_1 | Picard .dict File |
+| PICARD\_MACACA\_MULATTA\_ENSEMBL\_MMUL\_1 | Ensembl | Mmul\_1 | Picard .dict File |
+
+<span
+class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
+class="expand-control-text">Mus\_musculus</span>
+
+| Short Name | Source | Build | Type |
+|--------------------------------------|--------|--------|----------------------------|
+| BOWTIE\_MOUSE | NCBI | GRCm38 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE\_MUS\_MUSCULUS\_NCBI\_GRCM38 | NCBI | GRCm38 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_MOUSE | NCBI | GRCm38 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_MUS\_MUSCULUS\_NCBI\_GRCM38 | NCBI | GRCm38 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_MOUSE | NCBI | GRCm38 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_MUS\_MUSCULUS\_NCBI\_GRCM38 | NCBI | GRCm38 | Bwa\|Bowtie\|Bowtie2 Index |
+| CHR\_MOUSE | NCBI | GRCm38 | Chromosome Fasta Files |
+| CHR\_MUS\_MUSCULUS\_NCBI\_GRCM38 | NCBI | GRCm38 | Chromosome Fasta Files |
+| FAIDX\_MOUSE | NCBI | GRCm38 | Fasta Index .fai File |
+| FAIDX\_MUS\_MUSCULUS\_NCBI\_GRCM38 | NCBI | GRCm38 | Fasta Index .fai File |
+| GENOME\_MOUSE | NCBI | GRCm38 | Genome Fasta File |
+| GENOME\_MUS\_MUSCULUS\_NCBI\_GRCM38 | NCBI | GRCm38 | Genome Fasta File |
+| MOUSE | NCBI | GRCm38 | Main Directory |
+| MUS\_MUSCULUS\_NCBI\_GRCM38 | NCBI | GRCm38 | Main Directory |
+| PICARD\_MOUSE | NCBI | GRCm38 | Picard .dict File |
+| PICARD\_MUS\_MUSCULUS\_NCBI\_GRCM38 | NCBI | GRCm38 | Picard .dict File |
+
+<span
+class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
+class="expand-control-text">Mycobacterium\_tuberculosis\_H37RV</span>
+
+| Short Name | Source | Build | Type |
+|-----------------------------------------------------------------|--------|------------|----------------------------|
+| BOWTIE\_MYCOBACTERIUM\_TUBERCULOSIS\_H37RV | NCBI | 2001-09-07 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE\_MYCOBACTERIUM\_TUBERCULOSIS\_H37RV\_NCBI\_2001\_09\_07 | NCBI | 2001-09-07 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_MYCOBACTERIUM\_TUBERCULOSIS\_H37RV | NCBI | 2001-09-07 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_MYCOBACTERIUM\_TUBERCULOSIS\_H37RV\_NCBI\_2001\_09\_07 | NCBI | 2001-09-07 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_MYCOBACTERIUM\_TUBERCULOSIS\_H37RV | NCBI | 2001-09-07 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_MYCOBACTERIUM\_TUBERCULOSIS\_H37RV\_NCBI\_2001\_09\_07 | NCBI | 2001-09-07 | Bwa\|Bowtie\|Bowtie2 Index |
+| CHR\_MYCOBACTERIUM\_TUBERCULOSIS\_H37RV | NCBI | 2001-09-07 | Chromosome Fasta Files |
+| CHR\_MYCOBACTERIUM\_TUBERCULOSIS\_H37RV\_NCBI\_2001\_09\_07 | NCBI | 2001-09-07 | Chromosome Fasta Files |
+| FAIDX\_MYCOBACTERIUM\_TUBERCULOSIS\_H37RV | NCBI | 2001-09-07 | Fasta Index .fai File |
+| FAIDX\_MYCOBACTERIUM\_TUBERCULOSIS\_H37RV\_NCBI\_2001\_09\_07 | NCBI | 2001-09-07 | Fasta Index .fai File |
+| GENOME\_MYCOBACTERIUM\_TUBERCULOSIS\_H37RV | NCBI | 2001-09-07 | Genome Fasta File |
+| GENOME\_MYCOBACTERIUM\_TUBERCULOSIS\_H37RV\_NCBI\_2001\_09\_07 | NCBI | 2001-09-07 | Genome Fasta File |
+| MYCOBACTERIUM\_TUBERCULOSIS\_H37RV | NCBI | 2001-09-07 | Main Directory |
+| MYCOBACTERIUM\_TUBERCULOSIS\_H37RV\_NCBI\_2001\_09\_07 | NCBI | 2001-09-07 | Main Directory |
+| PICARD\_MYCOBACTERIUM\_TUBERCULOSIS\_H37RV | NCBI | 2001-09-07 | Picard .dict File |
+| PICARD\_MYCOBACTERIUM\_TUBERCULOSIS\_H37RV\_NCBI\_2001\_09\_07 | NCBI | 2001-09-07 | Picard .dict File |
+
+<span
+class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
+class="expand-control-text">Oryza\_sativa\_japonica</span>
+
+| Short Name | Source | Build | Type |
+|--------------------------------------------------------|---------|-----------|----------------------------|
+| BOWTIE\_ORYZA\_SATIVA\_JAPONICA\_ENSEMBL\_IRGSP\_1\_0 | Ensembl | IRGSP-1.0 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE\_RICE | Ensembl | IRGSP-1.0 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_ORYZA\_SATIVA\_JAPONICA\_ENSEMBL\_IRGSP\_1\_0 | Ensembl | IRGSP-1.0 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_RICE | Ensembl | IRGSP-1.0 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_ORYZA\_SATIVA\_JAPONICA\_ENSEMBL\_IRGSP\_1\_0 | Ensembl | IRGSP-1.0 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_RICE | Ensembl | IRGSP-1.0 | Bwa\|Bowtie\|Bowtie2 Index |
+| CHR\_ORYZA\_SATIVA\_JAPONICA\_ENSEMBL\_IRGSP\_1\_0 | Ensembl | IRGSP-1.0 | Chromosome Fasta Files |
+| CHR\_RICE | Ensembl | IRGSP-1.0 | Chromosome Fasta Files |
+| FAIDX\_ORYZA\_SATIVA\_JAPONICA\_ENSEMBL\_IRGSP\_1\_0 | Ensembl | IRGSP-1.0 | Fasta Index .fai File |
+| FAIDX\_RICE | Ensembl | IRGSP-1.0 | Fasta Index .fai File |
+| GENOME\_ORYZA\_SATIVA\_JAPONICA\_ENSEMBL\_IRGSP\_1\_0 | Ensembl | IRGSP-1.0 | Genome Fasta File |
+| GENOME\_RICE | Ensembl | IRGSP-1.0 | Genome Fasta File |
+| ORYZA\_SATIVA\_JAPONICA\_ENSEMBL\_IRGSP\_1\_0 | Ensembl | IRGSP-1.0 | Main Directory |
+| PICARD\_ORYZA\_SATIVA\_JAPONICA\_ENSEMBL\_IRGSP\_1\_0 | Ensembl | IRGSP-1.0 | Picard .dict File |
+| PICARD\_RICE | Ensembl | IRGSP-1.0 | Picard .dict File |
+| RICE | Ensembl | IRGSP-1.0 | Main Directory |
+
+<span
+class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
+class="expand-control-text">Pan\_troglodytes</span>
+
+| Short Name | Source | Build | Type |
+|--------------------------------------------|--------|----------|----------------------------|
+| BOWTIE\_PAN\_TROGLODYTES | NCBI | build3.1 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE\_PAN\_TROGLODYTES\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_PAN\_TROGLODYTES | NCBI | build3.1 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_PAN\_TROGLODYTES\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_PAN\_TROGLODYTES | NCBI | build3.1 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_PAN\_TROGLODYTES\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Bwa\|Bowtie\|Bowtie2 Index |
+| CHR\_PAN\_TROGLODYTES | NCBI | build3.1 | Chromosome Fasta Files |
+| CHR\_PAN\_TROGLODYTES\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Chromosome Fasta Files |
+| FAIDX\_PAN\_TROGLODYTES | NCBI | build3.1 | Fasta Index .fai File |
+| FAIDX\_PAN\_TROGLODYTES\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Fasta Index .fai File |
+| GENOME\_PAN\_TROGLODYTES | NCBI | build3.1 | Genome Fasta File |
+| GENOME\_PAN\_TROGLODYTES\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Genome Fasta File |
+| PAN\_TROGLODYTES | NCBI | build3.1 | Main Directory |
+| PAN\_TROGLODYTES\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Main Directory |
+| PICARD\_PAN\_TROGLODYTES | NCBI | build3.1 | Picard .dict File |
+| PICARD\_PAN\_TROGLODYTES\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Picard .dict File |
+
+<span
+class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
+class="expand-control-text">PhiX</span>
+
+| Short Name | Source | Build | Type |
+|------------------------------|----------|-------|----------------------------|
+| BOWTIE\_PHIX | Illumina | RTA | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE\_PHIX\_ILLUMINA\_RTA | Illumina | RTA | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_PHIX | Illumina | RTA | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_PHIX\_ILLUMINA\_RTA | Illumina | RTA | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_PHIX | Illumina | RTA | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_PHIX\_ILLUMINA\_RTA | Illumina | RTA | Bwa\|Bowtie\|Bowtie2 Index |
+| CHR\_PHIX | Illumina | RTA | Chromosome Fasta Files |
+| CHR\_PHIX\_ILLUMINA\_RTA | Illumina | RTA | Chromosome Fasta Files |
+| FAIDX\_PHIX | Illumina | RTA | Fasta Index .fai File |
+| FAIDX\_PHIX\_ILLUMINA\_RTA | Illumina | RTA | Fasta Index .fai File |
+| GENOME\_PHIX | Illumina | RTA | Genome Fasta File |
+| GENOME\_PHIX\_ILLUMINA\_RTA | Illumina | RTA | Genome Fasta File |
+| PHIX | Illumina | RTA | Main Directory |
+| PHIX\_ILLUMINA\_RTA | Illumina | RTA | Main Directory |
+| PICARD\_PHIX | Illumina | RTA | Picard .dict File |
+| PICARD\_PHIX\_ILLUMINA\_RTA | Illumina | RTA | Picard .dict File |
+
+<span
+class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
+class="expand-control-text">Pseudomonas\_aeruginosa\_PAO1</span>
+
+| Short Name | Source | Build | Type |
+|------------------------------------------------------------|--------|------------|----------------------------|
+| BOWTIE\_PSEUDOMONAS\_AERUGINOSA\_PAO1 | NCBI | 2000-09-13 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE\_PSEUDOMONAS\_AERUGINOSA\_PAO1\_NCBI\_2000\_09\_13 | NCBI | 2000-09-13 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_PSEUDOMONAS\_AERUGINOSA\_PAO1 | NCBI | 2000-09-13 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_PSEUDOMONAS\_AERUGINOSA\_PAO1\_NCBI\_2000\_09\_13 | NCBI | 2000-09-13 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_PSEUDOMONAS\_AERUGINOSA\_PAO1 | NCBI | 2000-09-13 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_PSEUDOMONAS\_AERUGINOSA\_PAO1\_NCBI\_2000\_09\_13 | NCBI | 2000-09-13 | Bwa\|Bowtie\|Bowtie2 Index |
+| CHR\_PSEUDOMONAS\_AERUGINOSA\_PAO1 | NCBI | 2000-09-13 | Chromosome Fasta Files |
+| CHR\_PSEUDOMONAS\_AERUGINOSA\_PAO1\_NCBI\_2000\_09\_13 | NCBI | 2000-09-13 | Chromosome Fasta Files |
+| FAIDX\_PSEUDOMONAS\_AERUGINOSA\_PAO1 | NCBI | 2000-09-13 | Fasta Index .fai File |
+| FAIDX\_PSEUDOMONAS\_AERUGINOSA\_PAO1\_NCBI\_2000\_09\_13 | NCBI | 2000-09-13 | Fasta Index .fai File |
+| GENOME\_PSEUDOMONAS\_AERUGINOSA\_PAO1 | NCBI | 2000-09-13 | Genome Fasta File |
+| GENOME\_PSEUDOMONAS\_AERUGINOSA\_PAO1\_NCBI\_2000\_09\_13 | NCBI | 2000-09-13 | Genome Fasta File |
+| PICARD\_PSEUDOMONAS\_AERUGINOSA\_PAO1 | NCBI | 2000-09-13 | Picard .dict File |
+| PICARD\_PSEUDOMONAS\_AERUGINOSA\_PAO1\_NCBI\_2000\_09\_13 | NCBI | 2000-09-13 | Picard .dict File |
+| PSEUDOMONAS\_AERUGINOSA\_PAO1 | NCBI | 2000-09-13 | Main Directory |
+| PSEUDOMONAS\_AERUGINOSA\_PAO1\_NCBI\_2000\_09\_13 | NCBI | 2000-09-13 | Main Directory |
+
+<span
+class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
+class="expand-control-text">Rattus\_norvegicus</span>
+
+| Short Name | Source | Build | Type |
+|-----------------------------------------------|--------|-----------|----------------------------|
+| BOWTIE\_RAT | NCBI | Rnor\_5.0 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE\_RATTUS\_NORVEGICUS\_NCBI\_RNOR\_5\_0 | NCBI | Rnor\_5.0 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE\_RATTUS\_NORVEGICUS\_NCBI\_RNOR\_6\_0 | NCBI | Rnor\_6.0 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_RAT | NCBI | Rnor\_5.0 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_RATTUS\_NORVEGICUS\_NCBI\_RNOR\_5\_0 | NCBI | Rnor\_5.0 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_RATTUS\_NORVEGICUS\_NCBI\_RNOR\_6\_0 | NCBI | Rnor\_6.0 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_RAT | NCBI | Rnor\_5.0 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_RATTUS\_NORVEGICUS\_NCBI\_RNOR\_5\_0 | NCBI | Rnor\_5.0 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_RATTUS\_NORVEGICUS\_NCBI\_RNOR\_6\_0 | NCBI | Rnor\_6.0 | Bwa\|Bowtie\|Bowtie2 Index |
+| CHR\_RAT | NCBI | Rnor\_5.0 | Chromosome Fasta Files |
+| CHR\_RATTUS\_NORVEGICUS\_NCBI\_RNOR\_5\_0 | NCBI | Rnor\_5.0 | Chromosome Fasta Files |
+| CHR\_RATTUS\_NORVEGICUS\_NCBI\_RNOR\_6\_0 | NCBI | Rnor\_6.0 | Chromosome Fasta Files |
+| FAIDX\_RAT | NCBI | Rnor\_5.0 | Fasta Index .fai File |
+| FAIDX\_RATTUS\_NORVEGICUS\_NCBI\_RNOR\_5\_0 | NCBI | Rnor\_5.0 | Fasta Index .fai File |
+| FAIDX\_RATTUS\_NORVEGICUS\_NCBI\_RNOR\_6\_0 | NCBI | Rnor\_6.0 | Fasta Index .fai File |
+| GENOME\_RAT | NCBI | Rnor\_5.0 | Genome Fasta File |
+| GENOME\_RATTUS\_NORVEGICUS\_NCBI\_RNOR\_5\_0 | NCBI | Rnor\_5.0 | Genome Fasta File |
+| GENOME\_RATTUS\_NORVEGICUS\_NCBI\_RNOR\_6\_0 | NCBI | Rnor\_6.0 | Genome Fasta File |
+| PICARD\_RAT | NCBI | Rnor\_5.0 | Picard .dict File |
+| PICARD\_RATTUS\_NORVEGICUS\_NCBI\_RNOR\_5\_0 | NCBI | Rnor\_5.0 | Picard .dict File |
+| PICARD\_RATTUS\_NORVEGICUS\_NCBI\_RNOR\_6\_0 | NCBI | Rnor\_6.0 | Picard .dict File |
+| RAT | NCBI | Rnor\_5.0 | Main Directory |
+| RATTUS\_NORVEGICUS\_NCBI\_RNOR\_5\_0 | NCBI | Rnor\_5.0 | Main Directory |
+| RATTUS\_NORVEGICUS\_NCBI\_RNOR\_6\_0 | NCBI | Rnor\_6.0 | Main Directory |
+
+<span
+class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
+class="expand-control-text">Saccharomyces\_cerevisiae</span>
+
+| Short Name | Source | Build | Type |
+|-----------------------------------------------------|--------|----------|----------------------------|
+| BOWTIE\_SACCHAROMYCES\_CEREVISIAE\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE\_YEAST | NCBI | build3.1 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_SACCHAROMYCES\_CEREVISIAE\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_YEAST | NCBI | build3.1 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_SACCHAROMYCES\_CEREVISIAE\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_YEAST | NCBI | build3.1 | Bwa\|Bowtie\|Bowtie2 Index |
+| CHR\_SACCHAROMYCES\_CEREVISIAE\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Chromosome Fasta Files |
+| CHR\_YEAST | NCBI | build3.1 | Chromosome Fasta Files |
+| FAIDX\_SACCHAROMYCES\_CEREVISIAE\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Fasta Index .fai File |
+| FAIDX\_YEAST | NCBI | build3.1 | Fasta Index .fai File |
+| GENOME\_SACCHAROMYCES\_CEREVISIAE\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Genome Fasta File |
+| GENOME\_YEAST | NCBI | build3.1 | Genome Fasta File |
+| PICARD\_SACCHAROMYCES\_CEREVISIAE\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Picard .dict File |
+| PICARD\_YEAST | NCBI | build3.1 | Picard .dict File |
+| SACCHAROMYCES\_CEREVISIAE\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Main Directory |
+| YEAST | NCBI | build3.1 | Main Directory |
+
+<span
+class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
+class="expand-control-text">Sorghum\_bicolor</span>
+
+| Short Name | Source | Build | Type |
+|------------------------------------------|---------|-------|----------------------------|
+| BOWTIE\_SORGHUM | Ensembl | Sbi1 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE\_SORGHUM\_BICOLOR\_ENSEMBL\_SBI1 | Ensembl | Sbi1 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_SORGHUM | Ensembl | Sbi1 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_SORGHUM\_BICOLOR\_ENSEMBL\_SBI1 | Ensembl | Sbi1 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_SORGHUM | Ensembl | Sbi1 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_SORGHUM\_BICOLOR\_ENSEMBL\_SBI1 | Ensembl | Sbi1 | Bwa\|Bowtie\|Bowtie2 Index |
+| CHR\_SORGHUM | Ensembl | Sbi1 | Chromosome Fasta Files |
+| CHR\_SORGHUM\_BICOLOR\_ENSEMBL\_SBI1 | Ensembl | Sbi1 | Chromosome Fasta Files |
+| FAIDX\_SORGHUM | Ensembl | Sbi1 | Fasta Index .fai File |
+| FAIDX\_SORGHUM\_BICOLOR\_ENSEMBL\_SBI1 | Ensembl | Sbi1 | Fasta Index .fai File |
+| GENOME\_SORGHUM | Ensembl | Sbi1 | Genome Fasta File |
+| GENOME\_SORGHUM\_BICOLOR\_ENSEMBL\_SBI1 | Ensembl | Sbi1 | Genome Fasta File |
+| PICARD\_SORGHUM | Ensembl | Sbi1 | Picard .dict File |
+| PICARD\_SORGHUM\_BICOLOR\_ENSEMBL\_SBI1 | Ensembl | Sbi1 | Picard .dict File |
+| SORGHUM | Ensembl | Sbi1 | Main Directory |
+| SORGHUM\_BICOLOR\_ENSEMBL\_SBI1 | Ensembl | Sbi1 | Main Directory |
+
+<span
+class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
+class="expand-control-text">Staphylococcus\_aureus\_NCTC\_8325</span>
+
+| Short Name | Source | Build | Type |
+|-----------------------------------------------------------------|--------|------------|----------------------------|
+| BOWTIE\_STAPHYLOCOCCUS\_AUREUS\_NCTC\_8325 | NCBI | 2006-02-13 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE\_STAPHYLOCOCCUS\_AUREUS\_NCTC\_8325\_NCBI\_2006\_02\_13 | NCBI | 2006-02-13 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_STAPHYLOCOCCUS\_AUREUS\_NCTC\_8325 | NCBI | 2006-02-13 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_STAPHYLOCOCCUS\_AUREUS\_NCTC\_8325\_NCBI\_2006\_02\_13 | NCBI | 2006-02-13 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_STAPHYLOCOCCUS\_AUREUS\_NCTC\_8325 | NCBI | 2006-02-13 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_STAPHYLOCOCCUS\_AUREUS\_NCTC\_8325\_NCBI\_2006\_02\_13 | NCBI | 2006-02-13 | Bwa\|Bowtie\|Bowtie2 Index |
+| CHR\_STAPHYLOCOCCUS\_AUREUS\_NCTC\_8325 | NCBI | 2006-02-13 | Chromosome Fasta Files |
+| CHR\_STAPHYLOCOCCUS\_AUREUS\_NCTC\_8325\_NCBI\_2006\_02\_13 | NCBI | 2006-02-13 | Chromosome Fasta Files |
+| FAIDX\_STAPHYLOCOCCUS\_AUREUS\_NCTC\_8325 | NCBI | 2006-02-13 | Fasta Index .fai File |
+| FAIDX\_STAPHYLOCOCCUS\_AUREUS\_NCTC\_8325\_NCBI\_2006\_02\_13 | NCBI | 2006-02-13 | Fasta Index .fai File |
+| GENOME\_STAPHYLOCOCCUS\_AUREUS\_NCTC\_8325 | NCBI | 2006-02-13 | Genome Fasta File |
+| GENOME\_STAPHYLOCOCCUS\_AUREUS\_NCTC\_8325\_NCBI\_2006\_02\_13 | NCBI | 2006-02-13 | Genome Fasta File |
+| PICARD\_STAPHYLOCOCCUS\_AUREUS\_NCTC\_8325 | NCBI | 2006-02-13 | Picard .dict File |
+| PICARD\_STAPHYLOCOCCUS\_AUREUS\_NCTC\_8325\_NCBI\_2006\_02\_13 | NCBI | 2006-02-13 | Picard .dict File |
+| STAPHYLOCOCCUS\_AUREUS\_NCTC\_8325 | NCBI | 2006-02-13 | Main Directory |
+| STAPHYLOCOCCUS\_AUREUS\_NCTC\_8325\_NCBI\_2006\_02\_13 | NCBI | 2006-02-13 | Main Directory |
+
+<span
+class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
+class="expand-control-text">Sus\_scrofa</span>
+
+| Short Name | Source | Build | Type |
+|------------------------------------------|--------|-------------|----------------------------|
+| BOWTIE\_PIG | NCBI | Sscrofa10.2 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE\_SUS\_SCROFA\_NCBI\_SSCROFA10\_2 | NCBI | Sscrofa10.2 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_PIG | NCBI | Sscrofa10.2 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_SUS\_SCROFA\_NCBI\_SSCROFA10\_2 | NCBI | Sscrofa10.2 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_PIG | NCBI | Sscrofa10.2 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_SUS\_SCROFA\_NCBI\_SSCROFA10\_2 | NCBI | Sscrofa10.2 | Bwa\|Bowtie\|Bowtie2 Index |
+| CHR\_PIG | NCBI | Sscrofa10.2 | Chromosome Fasta Files |
+| CHR\_SUS\_SCROFA\_NCBI\_SSCROFA10\_2 | NCBI | Sscrofa10.2 | Chromosome Fasta Files |
+| FAIDX\_PIG | NCBI | Sscrofa10.2 | Fasta Index .fai File |
+| FAIDX\_SUS\_SCROFA\_NCBI\_SSCROFA10\_2 | NCBI | Sscrofa10.2 | Fasta Index .fai File |
+| GENOME\_PIG | NCBI | Sscrofa10.2 | Genome Fasta File |
+| GENOME\_SUS\_SCROFA\_NCBI\_SSCROFA10\_2 | NCBI | Sscrofa10.2 | Genome Fasta File |
+| PICARD\_PIG | NCBI | Sscrofa10.2 | Picard .dict File |
+| PICARD\_SUS\_SCROFA\_NCBI\_SSCROFA10\_2 | NCBI | Sscrofa10.2 | Picard .dict File |
+| PIG | NCBI | Sscrofa10.2 | Main Directory |
+| SUS\_SCROFA\_NCBI\_SSCROFA10\_2 | NCBI | Sscrofa10.2 | Main Directory |
+
+<span
+class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
+class="expand-control-text">Zea\_mays</span>
+
+| Short Name | Source | Build | Type |
+|------------------------------------|---------|-------|----------------------------|
+| BOWTIE\_MAIZE | Ensembl | AGPv3 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE\_ZEA\_MAYS\_ENSEMBL\_AGPV3 | Ensembl | AGPv3 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_MAIZE | Ensembl | AGPv3 | Bwa\|Bowtie\|Bowtie2 Index |
+| BOWTIE2\_ZEA\_MAYS\_ENSEMBL\_AGPV3 | Ensembl | AGPv3 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_MAIZE | Ensembl | AGPv3 | Bwa\|Bowtie\|Bowtie2 Index |
+| BWA\_ZEA\_MAYS\_ENSEMBL\_AGPV3 | Ensembl | AGPv3 | Bwa\|Bowtie\|Bowtie2 Index |
+| CHR\_MAIZE | Ensembl | AGPv3 | Chromosome Fasta Files |
+| CHR\_ZEA\_MAYS\_ENSEMBL\_AGPV3 | Ensembl | AGPv3 | Chromosome Fasta Files |
+| FAIDX\_MAIZE | Ensembl | AGPv3 | Fasta Index .fai File |
+| FAIDX\_ZEA\_MAYS\_ENSEMBL\_AGPV3 | Ensembl | AGPv3 | Fasta Index .fai File |
+| GENOME\_MAIZE | Ensembl | AGPv3 | Genome Fasta File |
+| GENOME\_ZEA\_MAYS\_ENSEMBL\_AGPV3 | Ensembl | AGPv3 | Genome Fasta File |
+| MAIZE | Ensembl | AGPv3 | Main Directory |
+| PICARD\_MAIZE | Ensembl | AGPv3 | Picard .dict File |
+| PICARD\_ZEA\_MAYS\_ENSEMBL\_AGPV3 | Ensembl | AGPv3 | Picard .dict File |
+| ZEA\_MAYS\_ENSEMBL\_AGPV3 | Ensembl | AGPv3 | Main Directory |
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[biodata\_crane.xml](attachments/15171894/15171895.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[biodata\_crane\_Arabidopsis\_thaliana.xsl](attachments/15171894/15171896.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[biodata\_crane\_Bacillus\_cereus\_ATCC\_10987.xsl](attachments/15171894/15171897.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[biodata\_crane\_Bacillus\_subtilis\_168.xsl](attachments/15171894/15171898.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[biodata\_crane\_Bos\_taurus.xsl](attachments/15171894/15171899.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[biodata\_crane\_Caenorhabditis\_elegans.xsl](attachments/15171894/15171900.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[biodata\_crane\_Canis\_familiaris.xsl](attachments/15171894/15171901.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[biodata\_crane\_Danio\_rerio.xsl](attachments/15171894/15171902.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[biodata\_crane\_Drosophila\_melanogaster.xsl](attachments/15171894/15171903.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[biodata\_crane\_Enterobacteriophage\_lambda.xsl](attachments/15171894/15171904.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[biodata\_crane\_Equus\_caballus.xsl](attachments/15171894/15171905.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[biodata\_crane\_Escherichia\_coli\_K\_12\_DH10B.xsl](attachments/15171894/15171906.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[biodata\_crane\_Escherichia\_coli\_K\_12\_MG1655.xsl](attachments/15171894/15171907.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[biodata\_crane\_Gallus\_gallus.xsl](attachments/15171894/15171908.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[biodata\_crane\_Glycine\_max.xsl](attachments/15171894/15171909.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[biodata\_crane\_Homo\_sapiens.xsl](attachments/15171894/15171910.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[biodata\_crane\_Macaca\_mulatta.xsl](attachments/15171894/15171911.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[biodata\_crane\_Mus\_musculus.xsl](attachments/15171894/15171912.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[biodata\_crane\_Mycobacterium\_tuberculosis\_H37RV.xsl](attachments/15171894/15171913.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[biodata\_crane\_Oryza\_sativa\_japonica.xsl](attachments/15171894/15171914.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[biodata\_crane\_Pan\_troglodytes.xsl](attachments/15171894/15171915.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[biodata\_crane\_PhiX.xsl](attachments/15171894/15171916.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[biodata\_crane\_Pseudomonas\_aeruginosa\_PAO1.xsl](attachments/15171894/15171917.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[biodata\_crane\_Rattus\_norvegicus.xsl](attachments/15171894/15171918.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[biodata\_crane\_Saccharomyces\_cerevisiae.xsl](attachments/15171894/15171919.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[biodata\_crane\_Sorghum\_bicolor.xsl](attachments/15171894/15171920.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[biodata\_crane\_Staphylococcus\_aureus\_NCTC\_8325.xsl](attachments/15171894/15171921.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[biodata\_crane\_Sus\_scrofa.xsl](attachments/15171894/15171922.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[biodata\_crane\_Zea\_mays.xsl](attachments/15171894/15171923.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[biodata\_crane.xml](attachments/15171894/35324389.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[biodata\_crane.xml](attachments/15171894/35324388.xml) (text/xml)
+
+Document generated by Confluence on Oct 24, 2018 14:54
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/_index.md b/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/_index.md
new file mode 100644
index 00000000..e98f2b9f
--- /dev/null
+++ b/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/_index.md
@@ -0,0 +1,20 @@
++++
+title = "Data Manipulation Tools"
++++
+
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Running Applications](Running-Applications_7471153.html)
+5. [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
+
+<span id="title-text"> HCC-DOCS : Data Manipulation Tools </span>
+=================================================================
+
+Created by <span class="author"> Adam Caprez</span> on Sep 04, 2014
+
+
+
+Document generated by Confluence on Oct 24, 2018 14:50
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/bamtools/_index.md b/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/bamtools/_index.md
new file mode 100644
index 00000000..a85938e9
--- /dev/null
+++ b/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/bamtools/_index.md
@@ -0,0 +1,149 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Running Applications](Running-Applications_7471153.html)
+5. [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
+6. [Data Manipulation Tools](Data-Manipulation-Tools_8193304.html)
+
+<span id="title-text"> HCC-DOCS : BamTools </span>
+==================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified by
+<span class="editor"> Natasha Pavlovikj</span> on Sep 07, 2018
+
+| Name | Version | Resource |
+|----------|---------|----------|
+| bamtools | 2.3.0 | Tusker |
+| bamtools | 2.4.1 | Tusker |
+
+| | | |
+|----------|-------|-------|
+| bamtools | 2.3.0 | Crane |
+| bamtools | 2.4.1 | Crane |
+
+
+
+The SAM/BAM format is a standard format for short read alignments. While
+SAM is the plain-text version of the alignments, BAM is compressed,
+binary format of the alignments that is used for space-saving. BamTools
+is a toolkit for handling BAM files. BamTools provides a powerful suite
+of command-lines programs for manipulating and querying BAM files for
+data.
+
+The basic usage of BamTools is:
+
+**General BamTools Usage**
+
+``` syntaxhighlighter-pre
+bamtools COMMAND [options]
+```
+
+where **COMMAND** is one of the following BamTools commands**:**
+
+- **convert**: Converts between BAM and a number of other formats
+- **count**: Prints number of alignments in BAM file(s)
+- **coverage**: Prints coverage statistics from the input BAM file
+- **filter**: Filters BAM file(s) by user-specified criteria
+- **header**: Prints BAM header information
+- **index**: Generates index for BAM file
+- **merge**: Merge multiple BAM files into single file
+- **random**: Select random alignments from existing BAM file(s),
+ intended more as a testing tool
+- **resolve**: Resolves paired-end reads (marking the IsProperPair
+ flag as needed)
+- **revert**: Removes duplicate marks and restores original base
+ qualities
+- **sort**: Sorts the BAM file according to some criteria
+- **split**: Splits a BAM file on user-specified property, creating a
+ new BAM output file for each value found
+- **stats**: Prints some basic statistics from input BAM file(s)
+
+For detailed description and more information on a specific command,
+just type:
+
+**General BamTools COMMAND Options**
+
+``` syntaxhighlighter-pre
+[<username>@login.tusker~]$ bamtools help COMMAND
+```
+
+or check the BamTools web
+site: <a href="https://github.com/pezmaster31/bamtools/wiki" class="external-link">https://github.com/pezmaster31/bamtools/wiki</a>.
+
+The page [Running BamTools
+Commands](Running-BamTools-Commands_8193306.html) shows how to run
+BamTools on HCC.
+
+
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_bamtools\_version.xsl](attachments/8193305/8127591.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193305/8127592.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_bamtools\_version.xsl](attachments/8193305/8127593.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193305/8127594.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193305/35325459.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193305/35325485.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193305/35325504.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193305/35325537.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193305/35325874.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193305/35325893.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193305/35325921.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193305/35325940.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193305/35325971.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193305/35326029.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193305/35326100.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193305/35326213.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193305/35326315.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193305/35326409.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193305/35326437.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193305/35326505.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193305/35326555.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193305/35326594.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193305/35326645.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193305/35326667.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193305/35326825.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193305/35326902.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193305/35326937.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193305/35326956.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193305/35327038.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193305/35325385.xml) (text/xml)
+
+Document generated by Confluence on Oct 24, 2018 14:50
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/bamtools/running_bamtools_commands.md b/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/bamtools/running_bamtools_commands.md
new file mode 100644
index 00000000..38fd05d9
--- /dev/null
+++ b/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/bamtools/running_bamtools_commands.md
@@ -0,0 +1,287 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Running Applications](Running-Applications_7471153.html)
+5. [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
+6. [Data Manipulation Tools](Data-Manipulation-Tools_8193304.html)
+7. [BamTools](BamTools_8193305.html)
+
+<span id="title-text"> HCC-DOCS : Running BamTools Commands </span>
+===================================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified by
+<span class="editor"> Natasha Pavlovikj</span> on Sep 07, 2018
+
+**BamTools Convert:**
+
+One of the most frequently used BamTools command is **convert**.
+
+The basic usage of the BamTools **convert** is:
+
+**General BamTools Convert Usage**
+
+``` syntaxhighlighter-pre
+bamtools convert -format [bed|fasta|fastq|json|pileup|sam|yaml] -in input_alignments.bam -out output_reads.[bed|fasta|fastq|json|pileup|sam|yaml]
+```
+
+where the option **-format** specifies the type of the output
+file, **input\_alignments.bam** is the input BAM file,
+and **-out** defines the name and the type of the converted file.
+
+Running BamTools **convert** on Tusker with input
+file **input\_alignments.bam** and output
+file **output\_reads.fastq** is shown below:
+
+**bamtools\_convert.submit**
+
+\#!/bin/sh
+\#SBATCH --job-name=BamTools\_Convert
+\#SBATCH --nodes=1
+\#SBATCH --ntasks-per-node=1
+\#SBATCH --time=168:00:00
+\#SBATCH --mem=20gb
+\#SBATCH --output=BamTools.%J.out
+\#SBATCH --error=BamTools.%J.err
+
+
+
+| |
+|--------------------------|
+| module load bamtools/2.4 |
+
+bamtools convert -format fastq -in input\_alignments.bam -out
+output\_reads.fastq
+
+All BamTools commands are single threaded, and therefore both **\#SBATCH
+--nodes** and **\#SBATCH --ntasks-per-node** are set to **1**.
+
+
+
+**BamTools Count:**
+
+**BamTools Count Command**
+
+``` syntaxhighlighter-pre
+bamtools count -in input_alignments.bam
+```
+
+The command **bamtools count** outputs the total number of alignments in
+the BAM file.
+
+
+
+**BamTools Coverage:**
+
+**BamTools Coverage Command**
+
+``` syntaxhighlighter-pre
+bamtools coverage -in input_alignments.bam -out output_reads_coverage.txt
+```
+
+The command **bamtools coverage **prints the coverage data for a single
+BAM file
+
+
+
+**BamTools Filter:**
+
+**BamTools Filter Command**
+
+``` syntaxhighlighter-pre
+ bamtools filter -in input_alignments.bam -out output_alignments_filtered.bam -length 100
+```
+
+The command **bamtools filter** filters the BAM file based on specified
+options. In this example, the resulting bam
+file **output\_alignments\_filtered.bam** contains alignments with
+length more than 100.
+
+
+
+**BamTools Header:**
+
+**BamTools Header Command**
+
+``` syntaxhighlighter-pre
+ bamtools header -in input_alignments.bam -out output_alignments_header.txt
+```
+
+The command **bamtools header** prints the header from BAM file.
+
+
+
+**BamTools Index:**
+
+**BamTools Index Command**
+
+``` syntaxhighlighter-pre
+ bamtools index -in input_alignments.bam
+```
+
+The command **bamtools index** creates index for BAM file and prints
+**input\_alignments.bam.bai** file.
+
+
+
+**BamTools Merge:**
+
+**BamTools Merge Command**
+
+``` syntaxhighlighter-pre
+ bamtools merge -in input_alignments_1.bam -in input_alignments_2.bam -in input_alignments_3.bam -out output_alignments_merged.bam
+```
+
+The command **bamtools merge** merges multiple (more than 2) BAM files
+into one.
+
+
+
+**BamTools Random:**
+
+**BamTools Random Command**
+
+``` syntaxhighlighter-pre
+ bamtools random -in input_alignments.bam -out output_alignments_100.bam -n 100
+```
+
+The command **bamtools random** grabs a random subset of alignments.
+With the option **-n 100**, 100 randomly chosen alignments are stored in
+the output file **output\_alignments\_100.bam**.
+
+
+
+**BamTools Resolve:**
+
+**BamTools Resolve Command**
+
+``` syntaxhighlighter-pre
+ bamtools resolve -twoPass -in input_alignments.bam -out output_alignments.bam
+```
+
+The command **bamtools resolve** resolves paired-end reads. The
+resolving mode is required, and it can be **-makeStats**,
+**-markPairs**, or **-twoPass**.
+
+**
+**
+
+**BamTools Revert:**
+
+**BamTools Revert Command**
+
+``` syntaxhighlighter-pre
+ bamtools revert -in input_alignments.bam -out output_alignments_reverted.bam
+```
+
+The command **bamtools revert** removes duplicate marks and restores
+original base qualities.
+
+
+
+**BamTools Sort:**
+
+**BamTools Sort Command**
+
+``` syntaxhighlighter-pre
+ bamtools sort -in input_alignments.bam -out output_alignments_sorted.bam -byname
+```
+
+The command **bamtools sort** sorts a BAM file according to a given
+option. **Output\_alignments\_sorted.bam** is the resulting file, where
+the alignments are sorted by name.
+
+
+
+**BamTools Split:**
+
+**BamTools Split Command**
+
+``` syntaxhighlighter-pre
+ bamtools split -in input_alignments.bam -mapped
+```
+
+The command **bamtools split** splits BAM file on user-specified
+property and creates a new BAM output file for each value found. In the
+given example, an output file **input\_alignments.MAPPED.bam** is
+produced after -**mapped** split option is specified. Beside **mapped**,
+the split option can be: **-paired**, **-reference**, or **-tag
+<tag\_name>**.
+
+
+
+**BamTools Stats:**
+
+**BamTools Stats Command**
+
+``` syntaxhighlighter-pre
+ bamtools stats -in input_alignments.bam
+```
+
+The command **bamtools stats** prints general alignment statistics from
+the BAM file.
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[cb\_bamtools\_module.xsl](attachments/8193306/8127595.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193306/8127596.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193306/35325460.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193306/35325486.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193306/35325505.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193306/35325538.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193306/35325875.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193306/35325894.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193306/35325922.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193306/35325941.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193306/35325972.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193306/35326030.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193306/35326101.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193306/35326214.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193306/35326316.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193306/35326410.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193306/35326438.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193306/35326506.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193306/35326556.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193306/35326595.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193306/35326646.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193306/35326668.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193306/35326826.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193306/35326903.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193306/35326938.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193306/35326957.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193306/35327039.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193306/35325387.xml) (text/xml)
+
+Document generated by Confluence on Oct 24, 2018 14:50
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/samtools/_index.md b/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/samtools/_index.md
new file mode 100644
index 00000000..15d0fd9e
--- /dev/null
+++ b/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/samtools/_index.md
@@ -0,0 +1,1098 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Running Applications](Running-Applications_7471153.html)
+5. [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
+6. [Data Manipulation Tools](Data-Manipulation-Tools_8193304.html)
+
+<span id="title-text"> HCC-DOCS : SAMtools </span>
+==================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified by
+<span class="editor"> Natasha Pavlovikj</span> on Sep 07, 2018
+
+| Name | Version | Resource |
+|----------|---------|----------|
+| samtools | 0.1 | Tusker |
+| samtools | 1.1 | Tusker |
+| samtools | 1.2 | Tusker |
+| samtools | 1.3.1 | Tusker |
+
+| Name | Version | Resource |
+|----------|---------|----------|
+| samtools | 1.5 | Tusker |
+| samtools | 1.6 | Tusker |
+| samtools | 1.9 | Tusker |
+
+| | | |
+|----------|-------|-------|
+| samtools | 0.1 | Crane |
+| samtools | 1.1 | Crane |
+| samtools | 1.2 | Crane |
+| samtools | 1.3.1 | Crane |
+
+
+
+| | | |
+|----------|-----|-------|
+| samtools | 1.5 | Crane |
+| samtools | 1.6 | Crane |
+| samtools | 1.9 | Crane |
+
+The SAM format is a standard format for storing large nucleotide
+sequence alignments. The BAM format is just the binary form from SAM.
+SAMtools
+(<a href="http://samtools.sourceforge.net/" class="external-link">http://samtools.sourceforge.net/</a>)
+is a toolkit for manipulating alignments in SAM/BAM format, including
+sorting, merging, indexing and generating alignments in a per-position
+format.
+
+The basic usage of SAMtools is:
+
+**General SAMtools Usage**
+
+``` syntaxhighlighter-pre
+samtools COMMAND [options]
+```
+
+where **COMMAND** is one of the following SAMtools commands**:**
+
+- **view**: SAM/BAM and BAM/SAM conversion
+- **sort**: sort alignment file
+- **mpileup**: multi-way pileup
+- **depth**: compute the depth
+- **faidx**: index/extract FASTA
+- **tview**: text alignment viewer
+- **index**: index alignment
+- **idxstats**: BAM index stats
+- **fixmate**: fix mate information
+- **flagstat**: simple stats
+- **calmd**: recalculate MD/NM tags and '=' bases
+- **merge**: merge sorted alignments
+- **rmdup**: remove PCR duplicates
+- **reheader**: replace BAM header
+- **cat**: concatenate BAMs
+- **bedcov**: read depth per BED region
+- **targetcut**: cut fosmid regions
+- **phase**: phase heterozygotes
+- **bamshuf**: shuffle and group alignments by name
+
+For detailed description and more information on a specific command,
+just type:
+
+**General SAMtools COMMAND Options**
+
+``` syntaxhighlighter-pre
+[<username>@login.tusker~]$ samtools COMMAND
+```
+
+or check the SAMtools
+manual: <a href="http://samtools.sourceforge.net/samtools.shtml" class="external-link">http://samtools.sourceforge.net/samtools.shtml</a>.
+
+The page [Running SAMtools
+Commands](Running-SAMtools-Commands_8193308.html) shows how to run
+SAMtools on HCC.
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193307/8127597.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_samtools\_version.xsl](attachments/8193307/8127598.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193307/8127599.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_samtools\_version.xsl](attachments/8193307/8127600.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193307/17041705.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193307/17041737.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193307/17041794.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193307/17041865.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193307/17041827.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193307/17041920.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193307/17041952.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193307/17042008.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193307/17042041.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193307/17042093.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193307/17042126.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193307/17042213.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193307/17042246.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193307/17042298.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193307/17042331.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193307/17042391.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193307/17042424.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193307/17042480.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193307/17042549.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193307/17042516.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193307/17042603.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193307/17042636.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193307/17042712.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193307/17042745.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193307/17042798.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193307/17042831.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193307/17042939.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193307/17042887.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193307/17043006.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193307/17042973.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193307/17043068.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193307/17043101.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193307/17043204.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193307/17043152.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193307/17043237.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193307/17043294.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193307/17043327.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193307/17043381.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193307/17043414.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193307/17043477.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193307/17043546.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193307/17043513.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193307/17043599.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193307/17043632.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193307/17043720.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193307/17043753.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193307/17043805.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193307/17043838.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193307/17043899.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193307/17043932.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193307/17043989.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193307/17044022.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193307/17044074.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193307/17044141.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193307/17044108.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193307/17044195.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193307/17044228.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193307/17044282.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193307/17044315.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193307/17044376.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193307/17044413.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193307/17044480.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193307/17044517.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193307/17044576.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193307/17044613.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193307/17044673.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193307/17044710.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193307/17044773.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193307/17044810.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193307/17044926.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193307/17044963.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193307/17046995.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193307/17047032.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193307/18546771.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193307/18546702.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+
+Document generated by Confluence on Oct 24, 2018 14:50
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/samtools/running_bamtools_commands.md b/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/samtools/running_bamtools_commands.md
new file mode 100644
index 00000000..38fd05d9
--- /dev/null
+++ b/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/samtools/running_bamtools_commands.md
@@ -0,0 +1,287 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Running Applications](Running-Applications_7471153.html)
+5. [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
+6. [Data Manipulation Tools](Data-Manipulation-Tools_8193304.html)
+7. [BamTools](BamTools_8193305.html)
+
+<span id="title-text"> HCC-DOCS : Running BamTools Commands </span>
+===================================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified by
+<span class="editor"> Natasha Pavlovikj</span> on Sep 07, 2018
+
+**BamTools Convert:**
+
+One of the most frequently used BamTools command is **convert**.
+
+The basic usage of the BamTools **convert** is:
+
+**General BamTools Convert Usage**
+
+``` syntaxhighlighter-pre
+bamtools convert -format [bed|fasta|fastq|json|pileup|sam|yaml] -in input_alignments.bam -out output_reads.[bed|fasta|fastq|json|pileup|sam|yaml]
+```
+
+where the option **-format** specifies the type of the output
+file, **input\_alignments.bam** is the input BAM file,
+and **-out** defines the name and the type of the converted file.
+
+Running BamTools **convert** on Tusker with input
+file **input\_alignments.bam** and output
+file **output\_reads.fastq** is shown below:
+
+**bamtools\_convert.submit**
+
+\#!/bin/sh
+\#SBATCH --job-name=BamTools\_Convert
+\#SBATCH --nodes=1
+\#SBATCH --ntasks-per-node=1
+\#SBATCH --time=168:00:00
+\#SBATCH --mem=20gb
+\#SBATCH --output=BamTools.%J.out
+\#SBATCH --error=BamTools.%J.err
+
+
+
+| |
+|--------------------------|
+| module load bamtools/2.4 |
+
+bamtools convert -format fastq -in input\_alignments.bam -out
+output\_reads.fastq
+
+All BamTools commands are single threaded, and therefore both **\#SBATCH
+--nodes** and **\#SBATCH --ntasks-per-node** are set to **1**.
+
+
+
+**BamTools Count:**
+
+**BamTools Count Command**
+
+``` syntaxhighlighter-pre
+bamtools count -in input_alignments.bam
+```
+
+The command **bamtools count** outputs the total number of alignments in
+the BAM file.
+
+
+
+**BamTools Coverage:**
+
+**BamTools Coverage Command**
+
+``` syntaxhighlighter-pre
+bamtools coverage -in input_alignments.bam -out output_reads_coverage.txt
+```
+
+The command **bamtools coverage **prints the coverage data for a single
+BAM file
+
+
+
+**BamTools Filter:**
+
+**BamTools Filter Command**
+
+``` syntaxhighlighter-pre
+ bamtools filter -in input_alignments.bam -out output_alignments_filtered.bam -length 100
+```
+
+The command **bamtools filter** filters the BAM file based on specified
+options. In this example, the resulting bam
+file **output\_alignments\_filtered.bam** contains alignments with
+length more than 100.
+
+
+
+**BamTools Header:**
+
+**BamTools Header Command**
+
+``` syntaxhighlighter-pre
+ bamtools header -in input_alignments.bam -out output_alignments_header.txt
+```
+
+The command **bamtools header** prints the header from BAM file.
+
+
+
+**BamTools Index:**
+
+**BamTools Index Command**
+
+``` syntaxhighlighter-pre
+ bamtools index -in input_alignments.bam
+```
+
+The command **bamtools index** creates index for BAM file and prints
+**input\_alignments.bam.bai** file.
+
+
+
+**BamTools Merge:**
+
+**BamTools Merge Command**
+
+``` syntaxhighlighter-pre
+ bamtools merge -in input_alignments_1.bam -in input_alignments_2.bam -in input_alignments_3.bam -out output_alignments_merged.bam
+```
+
+The command **bamtools merge** merges multiple (more than 2) BAM files
+into one.
+
+
+
+**BamTools Random:**
+
+**BamTools Random Command**
+
+``` syntaxhighlighter-pre
+ bamtools random -in input_alignments.bam -out output_alignments_100.bam -n 100
+```
+
+The command **bamtools random** grabs a random subset of alignments.
+With the option **-n 100**, 100 randomly chosen alignments are stored in
+the output file **output\_alignments\_100.bam**.
+
+
+
+**BamTools Resolve:**
+
+**BamTools Resolve Command**
+
+``` syntaxhighlighter-pre
+ bamtools resolve -twoPass -in input_alignments.bam -out output_alignments.bam
+```
+
+The command **bamtools resolve** resolves paired-end reads. The
+resolving mode is required, and it can be **-makeStats**,
+**-markPairs**, or **-twoPass**.
+
+**
+**
+
+**BamTools Revert:**
+
+**BamTools Revert Command**
+
+``` syntaxhighlighter-pre
+ bamtools revert -in input_alignments.bam -out output_alignments_reverted.bam
+```
+
+The command **bamtools revert** removes duplicate marks and restores
+original base qualities.
+
+
+
+**BamTools Sort:**
+
+**BamTools Sort Command**
+
+``` syntaxhighlighter-pre
+ bamtools sort -in input_alignments.bam -out output_alignments_sorted.bam -byname
+```
+
+The command **bamtools sort** sorts a BAM file according to a given
+option. **Output\_alignments\_sorted.bam** is the resulting file, where
+the alignments are sorted by name.
+
+
+
+**BamTools Split:**
+
+**BamTools Split Command**
+
+``` syntaxhighlighter-pre
+ bamtools split -in input_alignments.bam -mapped
+```
+
+The command **bamtools split** splits BAM file on user-specified
+property and creates a new BAM output file for each value found. In the
+given example, an output file **input\_alignments.MAPPED.bam** is
+produced after -**mapped** split option is specified. Beside **mapped**,
+the split option can be: **-paired**, **-reference**, or **-tag
+<tag\_name>**.
+
+
+
+**BamTools Stats:**
+
+**BamTools Stats Command**
+
+``` syntaxhighlighter-pre
+ bamtools stats -in input_alignments.bam
+```
+
+The command **bamtools stats** prints general alignment statistics from
+the BAM file.
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[cb\_bamtools\_module.xsl](attachments/8193306/8127595.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193306/8127596.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193306/35325460.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193306/35325486.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193306/35325505.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193306/35325538.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193306/35325875.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193306/35325894.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193306/35325922.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193306/35325941.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193306/35325972.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193306/35326030.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193306/35326101.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193306/35326214.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193306/35326316.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193306/35326410.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193306/35326438.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193306/35326506.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193306/35326556.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193306/35326595.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193306/35326646.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193306/35326668.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193306/35326826.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193306/35326903.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193306/35326938.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193306/35326957.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193306/35327039.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[hcc\_modules.xml](attachments/8193306/35325387.xml) (text/xml)
+
+Document generated by Confluence on Oct 24, 2018 14:50
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/bioinformatics_tools/de_novo_assembly_tools/_index.md b/content/guides/running_applications/bioinformatics_tools/de_novo_assembly_tools/_index.md
new file mode 100644
index 00000000..37f8f108
--- /dev/null
+++ b/content/guides/running_applications/bioinformatics_tools/de_novo_assembly_tools/_index.md
@@ -0,0 +1,15 @@
++++
+title = "De Novo Assembly Tools"
++++
+
+<span id="title-text"> HCC-DOCS : De Novo Assembly Tools </span>
+================================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified by
+<span class="editor"> Natasha Pavlovikj</span> on Sep 04, 2014
+
+
+
+Document generated by Confluence on Oct 24, 2018 14:54
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/bioinformatics_tools/de_novo_assembly_tools/ray.md b/content/guides/running_applications/bioinformatics_tools/de_novo_assembly_tools/ray.md
new file mode 100644
index 00000000..d0e8f072
--- /dev/null
+++ b/content/guides/running_applications/bioinformatics_tools/de_novo_assembly_tools/ray.md
@@ -0,0 +1,242 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Running Applications](Running-Applications_7471153.html)
+5. [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
+6. [De Novo Assembly Tools](De-Novo-Assembly-Tools_8193280.html)
+
+<span id="title-text"> HCC-DOCS : Ray </span>
+=============================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified by
+<span class="editor"> Natasha Pavlovikj</span> on Dec 12, 2016
+
+| Name | Version | Resource |
+|------|---------|----------|
+| ray | 2.3 | Tusker |
+
+| | | |
+|-----|-----|-------|
+| ray | 2.3 | Crane |
+
+
+
+Ray
+(<a href="http://denovoassembler.sourceforge.net/" class="external-link">http://denovoassembler.sourceforge.net/</a>)
+is a de novo de Bruijn genome assembler that works with next-generation
+sequencing data (Illumina, 454, SOLiD). Ray is scalable and parallel
+software that takes advantage of multiple nodes and multiple CPUs using
+MPI (message passing interface).
+
+Ray can be used for building multiple applications:
+
+- <span style="line-height: 1.4285715;">de novo genome assembly</span>
+- de novo meta-genome assembly
+
+- de novo transcriptome assembly
+- quantification of contig abundances, microbiome consortia members,
+ transcript expression
+- taxonomy and gene ontology profiling of samples
+- comparing DNA samples using words
+
+
+In order to see all options available for running Ray, just type:
+
+**Ray Options**
+
+``` syntaxhighlighter-pre
+[<username>@login.tusker ~]$ mpiexec Ray -help
+```
+
+All options used for Ray can be defined in the command line:
+
+**General Ray Usage**
+
+``` syntaxhighlighter-pre
+[<username>@login.tusker ~]$ mpiexec Ray -k <kmer_value> -p input_reads_pair_1.[fa|fq] input_reads_pair_2.[fa|fq] -s input_reads.[fa|fq] -o <output_directory>
+```
+
+or can be stored in a configuration file *.conf* (one option per line):
+
+**General Ray Usage with Configuration File**
+
+``` syntaxhighlighter-pre
+[<username>@login.tusker ~]$ mpiexec Ray Ray.conf
+```
+
+Ray supports both paired-end (*-p*) and single-end reads (*-s*).
+Moreover, Ray can detect the input files automatically if the input
+directory is provided (*-detect-sequence-files input\_directory*). Ray
+supports odd values for k-mer larger or equal to 21 (*-k
+<kmer\_value>*). Ray supports multiple file formats: **fasta**,
+**fa**, **fasta.gz**, **fa.gz**, **fasta.bz2**, **fa.bz2**, **fastq**,
+**fq**, **fastq.gz**, **fq.gz**, **fastq.bz2**, **fq.bz2**, **sff**,
+**csfasta**, **csfa**.
+
+
+Simple SLURM script for running Ray on Tusker with both paired-end and
+single-end data with **k-mer=31**, **8 CPUs** and **4 GB RAM per
+CPU** is shown below:
+
+**ray.submit**
+
+\#!/bin/sh
+\#SBATCH --job-name=Ray
+\#SBATCH --ntasks=8
+\#SBATCH --time=168:00:00
+\#SBATCH --mem-per-cpu=4gb
+\#SBATCH --output=Ray.%J.out
+\#SBATCH --error=Ray.%J.err
+
+
+
+| |
+|--------------------------------------------------|
+| module load compiler/gcc/4.7 openmpi/1.6 ray/2.3 |
+
+mpiexec Ray -k 31 -p input\_reads\_pair\_1.fastq
+input\_reads\_pair\_2.fastq -s input\_reads.fasta -o output\_directory
+
+where **input\_reads\_pair\_1.fastq**
+and **input\_reads\_pair\_2.fastq** are the paired-end input files in
+**fastq** format, while **input\_reads.fasta** is the single-end input
+file in **fasta** format.
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-warning confluence-information-macro-icon"></span>
+
+ It is **not** necessary to specify the number of processes with
+the `-n `option to `mpiexec`. OpenMPI will determine that automatically
+from SLURM based on the value of the `--ntasks `option.
+
+
+
+**Ray Output**
+
+In the output folder (*-o **output\_directory*) Ray prints a lot of
+files with information about different steps and statistics from the
+execution process. Information about all output files can be found in
+Ray's manual. One of the most important results are:
+
+- <span
+ style="line-height: 1.4285715;">**Scaffolds.fasta**: </span>scaffold
+ sequences in FASTA format
+- <span style="line-height: 1.4285715;">**ScaffoldComponents.txt**:
+ components of each scaffold</span>
+- <span style="line-height: 1.4285715;">**Contigs.fasta**: contiguous
+ sequences in FASTA format </span>
+- <span style="line-height: 1.4285715;">**OutputNumbers.txt**: overall
+ numbers for the assembly</span>
+
+
+
+**Useful Information**
+
+In order to test the Ray performance on Tusker, we used three paired-end
+input fastq
+files: **small\_1.fastq**, **small\_2.fastq**, **medium\_1.fastq**, **medium\_2.fastq**, **large\_1.fastq**, **large\_2.fastq**.
+Some statistics about the input files and the time and memory resources
+required for Ray are shown on the table below:
+
+
+
+**total \# of sequences**
+
+**total \# of bases**
+
+**total size in MB**
+
+**RAY required time**
+
+**RAY required memory**
+
+\# of used CPUs
+
+**small\_1.fastq**
+
+50,121
+
+2,506,050
+
+8.010 MB
+
+\~ 3 minutes
+
+\~ 1 GB
+
+8
+
+**small\_2.fastq**
+
+50,121
+
+2,506,050
+
+8.010 MB
+
+**medium\_1.fastq**
+
+786,742
+
+59,792,392
+
+152 MB
+
+\~ 15 minutes
+
+\~ 1.5 GB
+
+8
+
+**medium\_2.fastq**
+
+786,742
+
+59,792,392
+
+152 MB
+
+**large\_1.fastq**
+
+10,174,715
+
+1,027,646,215
+
+3,376 MB
+
+\~ 5 hours
+
+\~ 17 GB
+
+8
+
+**large\_2.fastq**
+
+10,174,715
+
+1,027,646,215
+
+3,376 MB
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_ray\_version.xsl](attachments/9470322/9863497.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_ray\_version.xsl](attachments/9470322/9863498.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[cb\_ray\_module.xsl](attachments/9470322/9863499.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/9470322/9863500.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/9470322/9863501.xml)
+(application/octet-stream)
+
+Document generated by Confluence on Oct 24, 2018 14:54
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/bioinformatics_tools/de_novo_assembly_tools/soapdenovo2.md b/content/guides/running_applications/bioinformatics_tools/de_novo_assembly_tools/soapdenovo2.md
new file mode 100644
index 00000000..88caaa00
--- /dev/null
+++ b/content/guides/running_applications/bioinformatics_tools/de_novo_assembly_tools/soapdenovo2.md
@@ -0,0 +1,291 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Running Applications](Running-Applications_7471153.html)
+5. [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
+6. [De Novo Assembly Tools](De-Novo-Assembly-Tools_8193280.html)
+
+<span id="title-text"> HCC-DOCS : SOAPdenovo2 </span>
+=====================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified by
+<span class="editor"> Natasha Pavlovikj</span> on Dec 12, 2016
+
+| Name | Version | Resource |
+|-------------|---------|----------|
+| soapdenovo2 | r240 | Tusker |
+
+| | | |
+|-------------|------|-------|
+| soapdenovo2 | r240 | Crane |
+
+
+
+SOAPdenovo
+(<a href="http://soap.genomics.org.cn/soapdenovo.html" class="external-link">http://soap.genomics.org.cn/soapdenovo.html</a>) is
+a de novo genome assembler for short reads. It is specially designed for
+Illumina GA short reads and large plant and animal genomes. SOAPdenovo2
+is a newer version of SOAPdenovo with improved algorithm that reduces
+memory consumption, resolves more repeat regions, increases coverage,
+and optimizes the assembly for large genomes.
+
+SOAPdenovo2 has two commands, **SOAPdenovo-63mer** and
+**SOAPdenovo-127mer**. The first one is suitable for assembly with k-mer
+values less than 63 bp, requires less memory and runs faster. The latter
+one works for k-mer values less than 127 bp.
+
+In order to see the options available for **SOAPdenovo-63mer** just
+type:
+
+**SOAPdenovo-63mer Options**
+
+``` syntaxhighlighter-pre
+[<username>@login.tusker ~]$ SOAPdenovo-63mer
+```
+
+SOAPdenovo2 provides a mechanism to run the whole workflow at once, or
+in 5 separate steps.
+The basic usage of SOAPdenovo2 is:
+
+**General SOAPdenovo-63mer Usage**
+
+``` syntaxhighlighter-pre
+[<username>@login.tusker ~]$ SOAPdenovo-63mer all -s configFile -o output_directory/outputGraph -K <kmer_value> [options]
+```
+
+where **configFile** is a defined configuration file, **outputGraph** is
+the prefix of the output files, and **kmer\_value** is the value of
+k-mer used for building the assembly (<=63 for SOAPdenovo-63mer and
+<=127 for SOAPdenovo-127mer).
+
+If you want to run the assembly process step by step, then use the
+following sequential commands:
+
+**Step 1:**
+
+**SOAPdenovo2 Step 1 Options**
+
+``` syntaxhighlighter-pre
+SOAPdenovo-63mer pregraph -s configFile -o outputGraph [options]
+OR
+SOAPdenovo-63mer sparse_pregraph -s configFile -K <kmer_value> -z <genome_size> -o outputGraph [options]
+```
+
+**Step 2: **
+
+**SOAPdenovo2 Step 2 Options**
+
+``` syntaxhighlighter-pre
+SOAPdenovo-63mer contig -g inputGraph [options]
+```
+
+**Step 3:**
+
+**SOAPdenovo2 Step 3 Options**
+
+``` syntaxhighlighter-pre
+SOAPdenovo-63mer map -s configFile -g inputGraph [options]
+```
+
+**Step 4:**
+
+**SOAPdenovo2 Step 4 Options**
+
+``` syntaxhighlighter-pre
+SOAPdenovo-63mer scaff -g inputGraph [options]
+```
+
+As you can notice from the commands above, in order to run SOAPdenovo2,
+you first need to create a config file (**configFile**) that contains
+different information about the read files (*read length*, *insert
+size*, *reads location*). SOAPdenovo2 accepts read files in 3 formats:
+fasta, fastq and bam.
+
+The example configuration file **configFile** for 2 paired-end fastq
+files, 1 paired-end fasta file and 1 single-end fastq file looks like
+this:
+
+**configFile**
+
+<span style="color: rgb(0,0,0);">\#maximal read length</span>
+<span style="color: rgb(0,0,0);">max\_rd\_len=150</span>
+<span style="color: rgb(0,0,0);">\[LIB\]</span>
+<span style="color: rgb(0,0,0);">\#average insert size of the
+library</span>
+<span style="color: rgb(0,0,0);">avg\_ins=300</span>
+<span style="color: rgb(0,0,0);">\#if sequences are forward-reverse of
+reverse-forward</span>
+<span style="color: rgb(0,0,0);">reverse\_seq=0</span>
+<span style="color: rgb(0,0,0);">\#in which part(s) the reads are used
+(only contigs, only scaffolds, both contigs and scaffolds, only gap
+closure)</span>
+<span style="color: rgb(0,0,0);">asm\_flags=3</span>
+<span style="color: rgb(0,0,0);">\#cut the reads to the given
+length</span>
+<span style="color: rgb(0,0,0);">rd\_len\_cutoff=100</span>
+<span style="color: rgb(0,0,0);">\#in which order the reads are used
+while scaffolding</span>
+<span style="color: rgb(0,0,0);">rank=1</span>
+<span style="color: rgb(0,0,0);">\# cutoff of pair number for a reliable
+connection (at least 3 for short insert size)</span>
+<span style="color: rgb(0,0,0);">pair\_num\_cutoff=3</span>
+<span style="color: rgb(0,0,0);">\#minimum aligned length to contigs for
+a reliable read location (at least 32 for short insert size)</span>
+<span style="color: rgb(0,0,0);">map\_len=32</span>
+<span style="color: rgb(0,0,0);">\#paired-end fastq files, read 1 file
+should always be followed by read 2 file</span>
+<span style="color: rgb(0,0,0);">q1=input\_reads1\_pair\_1.fq</span>
+<span style="color: rgb(0,0,0);">q2=input\_reads1\_pair\_2.fq</span>
+<span style="color: rgb(0,0,0);">\#another pair of paired-end fastq
+files, read 1 file should always be followed by read 2 file</span>
+<span style="color: rgb(0,0,0);">q1=input\_reads2\_pair\_1.fq</span>
+<span style="color: rgb(0,0,0);">q2=input\_reads2\_pair\_2.fq</span>
+<span style="color: rgb(0,0,0);">\#paired-end fasta files, read 1 file
+should always be followed by read 2 file</span>
+<span style="color: rgb(0,0,0);">f1=input\_reads\_pair\_1.fa</span>
+<span style="color: rgb(0,0,0);">f2=input\_reads\_pair\_2.fa</span>
+<span style="color: rgb(0,0,0);">\#fastq file for single reads</span>
+<span style="color: rgb(0,0,0);">q=input\_reads.fq</span>
+
+After creating the configuration file **configFile**, the next step is
+to run the assembler using this file.
+Simple SLURM script for running SOAPdenovo2 with **k-mer=31**, **8
+CPUSs** and **50GB of RAM** on Tusker is shown below:
+
+**soapdenovo2.submit**
+
+\#!/bin/sh
+\#SBATCH --job-name=SOAPdenovo2
+\#SBATCH --nodes=1
+\#SBATCH --ntasks-per-node=8
+\#SBATCH --time=168:00:00
+\#SBATCH --mem=50gb
+\#SBATCH --output=SOAPdenovo2.%J.out
+\#SBATCH --error=SOAPdenovo2.%J.err
+
+
+| |
+|------------------------------|
+| module load soapdenovo2/r240 |
+
+SOAPdenovo-63mer all -s configFile -K 31 -o output\_directory/output31
+-p $SLURM\_NTASKS\_PER\_NODE
+
+
+
+**SOAPdenovo2 Output**
+
+SOAPdenovo2 outputs number of files in its *output\_directory/* after
+each executed step. The final assembly output is in the **.contig**
+file.
+
+**Output Directory After SOAPdenovo2**
+
+``` syntaxhighlighter-pre
+[<username>@login.tusker output_directory]$ ls
+output31.Arc output31.ContigIndex output31.gapSeq output31.newContigInde
+output31.bubbleInScaff output31.contigPosInscaff output31.kmerFreq output31.peGrads
+output31.contig output31.edge.gz output31.links output31.preArc
+```
+
+**
+**
+
+**Useful Information**
+
+In order to test the SOAPdenovo2 (soapdenovo2/r240) performance on
+Tusker, we used three different size input files. Some statistics about
+these input files and the time and memory resources required for
+SOAPdenovo2 are shown on the table below:
+
+
+
+**total \# of sequences**
+
+**total \# of bases**
+
+**total size in GB**
+
+SOAPdenovo2 required memory
+
+SOAPdenovo2 required time
+
+K-mer value
+
+\# of used CPUs
+
+**Input Data 1**
+
+49,720,374
+
+7,295,342,636
+
+10 GB
+
+\~ 32 GB
+
+\~ 1.5 hours
+
+31
+
+8
+
+**Input Data 2**
+
+166,040,440
+
+25,072,106,440
+
+62 GB
+
+\~ 125 GB
+
+\~ 6.5 hours
+
+31
+
+8
+
+**Input Data 3**
+
+318,681,730
+
+48,120,941,230
+
+115 GB
+
+\~ 125 GB
+
+\~ 13 hours
+
+31
+
+8
+
+In general, SOAPdenovo2 is a memory intensive assembler that requires
+approximately 30\~60 GB memory for assembling 50 million reads.
+Moreover, SOAPdenovo2 is a fast assembler and it takes around an hour to
+assemble 50 million reads.
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_soapdenovo2\_version.xsl](attachments/9470140/9863306.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_soapdenovo2\_version.xsl](attachments/9470140/9863307.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[cb\_soapdenovo2\_module.xsl](attachments/9470140/9863308.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/9470140/9863309.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/9470140/9863310.xml)
+(application/octet-stream)
+
+Document generated by Confluence on Oct 24, 2018 14:54
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/bioinformatics_tools/de_novo_assembly_tools/trinity/_index.md b/content/guides/running_applications/bioinformatics_tools/de_novo_assembly_tools/trinity/_index.md
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--- /dev/null
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@@ -0,0 +1,267 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Running Applications](Running-Applications_7471153.html)
+5. [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
+6. [De Novo Assembly Tools](De-Novo-Assembly-Tools_8193280.html)
+
+<span id="title-text"> HCC-DOCS : Trinity </span>
+=================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified by
+<span class="editor"> Natasha Pavlovikj</span> on Feb 26, 2018
+
+| Name | Version | Resource |
+|---------|---------------|----------|
+| trinity | r2013-02-25 | Tusker |
+| trinity | r2013-11-10 | Tusker |
+| trinity | r2014-04-13p1 | Tusker |
+
+| | | |
+|---------|---------------|-------|
+| trinity | r2013-11-10 | Crane |
+| trinity | r2014-04-13p1 | Crane |
+
+
+
+Trinity
+(<a href="http://trinityrnaseq.sourceforge.net/" class="external-link">http://trinityrnaseq.sourceforge.net/</a>)
+is a method for efficient and robust de novo reconstruction of
+transcriptomes from RNA-Seq data. Trinity combines three independent
+software modules: Inchworm, Chrysalis, and Butterfly. All these modules
+can be applied sequentially to process large RNA-Seq datasets.
+
+The basic usage of Trinity is:
+
+**General Trinity Usage**
+
+``` syntaxhighlighter-pre
+Trinity --seqType [fa|fq] --JM <jellyfish_memory> --left input_reads_pair_1.[fa|fq] --right input_reads_pair_2.[fa|fq] [options]
+```
+
+where **input\_reads\_pair\_1.\[fa\|fq\]**
+and **input\_reads\_pair\_2.\[fa\|fq\]** are the input paired-end files
+of sequence reads in fasta/fastq format, and **--seqType** is the type
+of these input reads. The option **--JM** defines the number of GB of
+system memory required for k-mer counting by jellyfish. Additional
+Trinity **options** can be found in the Trinity website, or by typing:
+
+**Additional Trinity Options**
+
+``` syntaxhighlighter-pre
+[<username>@login.tusker ~]$ Trinity
+```
+
+Running the Trinity pipeline from beginning to end on large datasets may
+exceed the walltime limit for a single job. Therefore, Trinity provides
+a mechanism to run the workflow in four separate steps, where each step
+resumes from the previous one. The same Trinity command and options are
+run for each step, with difference of an additional option that is
+included for the different steps. On the last step, the Trinity command
+is run as normal.
+
+**Step 1:**
+
+**Trinity Step 1 Options**
+
+``` syntaxhighlighter-pre
+Trinity.pl [options] --no_run_chrysalis
+```
+
+**Step 2: **
+
+**Trinity Step 2 Options**
+
+``` syntaxhighlighter-pre
+Trinity.pl [options] --no_run_quantifygraph
+```
+
+**Step 3:**
+
+**Trinity Step 3 Options**
+
+``` syntaxhighlighter-pre
+Trinity.pl [options] --no_run_butterfly
+```
+
+**Step 4:**
+
+**Trinity Step 4 Options**
+
+``` syntaxhighlighter-pre
+Trinity.pl [options]
+```
+
+Each step may be run as its own job, providing a workaround for the
+single job walltime limit. The following page describes how to run each
+step of Trinity as a single job under the SLURM scheduler on HCC:
+
+
+
+**Useful Information**
+
+In order to test the TRINITY (trinity/r2014-04-13p1) performance on
+Tusker, we used three paired-end input fastq files: **small\_1.fastq**,
+**small\_2.fastq**, **medium\_1.fastq**, **medium\_2.fastq**,
+**large\_1.fastq**, **large\_2.fastq. **Some statistics about the input
+files and the time and memory resources required for TRINITY are shown
+on the table below:
+
+
+
+**total \# of sequences**
+
+**total \# of bases**
+
+**total size in MB**
+
+**Trinity Step 1 required time**
+
+**Trinity Step 1 required memory**
+
+Trinity Step 2 required time
+
+Trinity Step 2 required memory
+
+Trinity Step 3 required time
+
+Trinity Step 3 required memory
+
+Trinity Step 4 required time
+
+Trinity Step 4 required memory
+
+\# of used CPUs
+
+**small\_1.fastq**
+
+50,121
+
+2,506,050
+
+8.010 MB
+
+\~ 1 minute
+
+\~ 35 GB
+
+\~ 0.01 hours
+
+\~ 0.6 GB
+
+\~ 0.2 minutes
+
+\~ 0.07 GB
+
+\~ 0.008 hours
+
+\~ 0.8 GB
+
+8
+
+**small\_2.fastq**
+
+50,121
+
+2,506,050
+
+8.010 MB
+
+**medium\_1.fastq**
+
+786,742
+
+59,792,392
+
+152 MB
+
+\~ 3 minutes
+
+\~ 68 GB
+
+\~ 0.1 hours
+
+\~ 3 GB
+
+\~ 0.8 minutes
+
+\~ 0.6 GB
+
+\~ 0.3 hours
+
+\~ 5 GB
+
+8
+
+**medium\_2.fastq**
+
+786,742
+
+59,792,392
+
+152 MB
+
+**large\_1.fastq**
+
+10,174,715
+
+1,027,646,215
+
+3,376 MB
+
+\~ 58 minutes
+
+\~ 80 GB
+
+\~ 5 hours
+
+\~ 30 GB
+
+\~ 35 minutes
+
+\~ 8 GB
+
+\~ 13 hours
+
+\~ 30 GB
+
+8
+
+**large\_2.fastq**
+
+10,174,715
+
+1,027,646,215
+
+3,376 MB
+
+Memory Requirement
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-warning confluence-information-macro-icon"></span>
+
+<span style="color: rgb(0,0,0);">The Inchworm (step 1) and Chrysalis
+(step 2) steps can be memory intensive. A basic recommendation is to
+have **1GB of RAM per 1M** </span><span
+style="color: rgb(0,0,0);">**\~76 base Illumina paired-end
+reads**.</span>
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193286/8127532.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_trinity\_version.xsl](attachments/8193286/8127533.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193286/8127534.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_trinity\_version.xsl](attachments/8193286/8127535.xsl)
+(application/octet-stream)
+
+Document generated by Confluence on Oct 24, 2018 14:54
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/bioinformatics_tools/de_novo_assembly_tools/trinity/running_trinity_in_multiple_steps.md b/content/guides/running_applications/bioinformatics_tools/de_novo_assembly_tools/trinity/running_trinity_in_multiple_steps.md
new file mode 100644
index 00000000..a513a0f7
--- /dev/null
+++ b/content/guides/running_applications/bioinformatics_tools/de_novo_assembly_tools/trinity/running_trinity_in_multiple_steps.md
@@ -0,0 +1,163 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Running Applications](Running-Applications_7471153.html)
+5. [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
+6. [De Novo Assembly Tools](De-Novo-Assembly-Tools_8193280.html)
+7. [Trinity](Trinity_8193286.html)
+
+<span id="title-text"> HCC-DOCS : Running Trinity in Multiple Steps </span>
+===========================================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified by
+<span class="editor"> Natasha Pavlovikj</span> on Dec 12, 2016
+
+**Running Trinity with Paired-End fastq data with 8 CPUs and 100GB of
+RAM**
+
+<span style="color: rgb(0,0,0);">The first step of running Trinity is to
+run Trinity with the option **--no\_run\_chrysalis**:</span>
+
+**trinity\_step1.submit**
+
+\#!/bin/sh
+\#SBATCH --job-name=Trinity\_Step1
+\#SBATCH --nodes=1
+\#SBATCH --ntasks-per-node=8
+\#SBATCH --time=168:00:00
+\#SBATCH --mem=100gb
+\#SBATCH --output=Trinity\_Step1.%J.out
+\#SBATCH --error=Trinity\_Step1.%J.err
+
+
+
+| |
+|-------------------------------------------------------------|
+| module load bowtie/1.0.0 samtools/0.1 trinity/r2014-04-13p1 |
+
+Trinity --seqType fq --JM 100G --left input\_reads\_pair\_1.fastq
+--right input\_reads\_pair\_2.fastq --SS\_lib\_type FR --output
+trinity\_out/ --CPU $SLURM\_NTASKS\_PER\_NODE --no\_run\_chrysalis
+
+<span style="color: rgb(0,0,0);">
+</span>
+
+<span style="color: rgb(0,0,0);">The second step of running Trinity is
+to run Trinity with the option </span><span
+style="color: rgb(0,0,0);"> </span><span
+style="color: rgb(0,0,0);"> </span>**--no\_run\_quantifygraph**<span
+style="color: rgb(0,0,0);">:</span>
+
+**trinity\_step2.submit**
+
+\#!/bin/sh
+\#SBATCH --job-name=Trinity\_Step2
+\#SBATCH --nodes=1
+\#SBATCH --ntasks-per-node=8
+\#SBATCH --time=168:00:00
+\#SBATCH --mem=100gb
+\#SBATCH --output=Trinity\_Step2.%J.out
+\#SBATCH --error=Trinity\_Step2.%J.err
+
+
+
+| |
+|-------------------------------------------------------------|
+| module load bowtie/1.0.0 samtools/0.1 trinity/r2014-04-13p1 |
+
+Trinity --seqType fq --JM 100G --left input\_reads\_pair\_1.fastq
+--right input\_reads\_pair\_2.fastq --SS\_lib\_type FR --output
+trinity\_out/ --CPU $SLURM\_NTASKS\_PER\_NODE --no\_run\_quantifygraph
+
+<span style="color: rgb(0,0,0);">
+</span>
+
+<span style="color: rgb(0,0,0);">The third step of running Trinity is to
+run Trinity with the option </span><span
+style="line-height: 1.4285715;"> **--no\_run\_butterfly**:</span>
+
+**trinity\_step3.submit**
+
+\#!/bin/sh
+\#SBATCH --job-name=Trinity\_Step3
+\#SBATCH --nodes=1
+\#SBATCH --ntasks-per-node=8
+\#SBATCH --time=168:00:00
+\#SBATCH --mem=100gb
+\#SBATCH --output=Trinity\_Step3.%J.out
+\#SBATCH --error=Trinity\_Step3.%J.err
+
+
+
+| |
+|-------------------------------------------------------------|
+| module load bowtie/1.0.0 samtools/0.1 trinity/r2014-04-13p1 |
+
+Trinity --seqType fq --JM 100G --left input\_reads\_pair\_1.fastq
+--right input\_reads\_pair\_2.fastq --SS\_lib\_type FR --output
+trinity\_out/ --CPU $SLURM\_NTASKS\_PER\_NODE --no\_run\_butterfly
+
+<span style="line-height: 1.4285715;">
+</span>
+
+<span style="color: rgb(0,0,0);">The fourth step of running Trinity is
+to run Trinity without any additional option</span><span
+style="color: rgb(0,0,0);">:</span>
+
+**trinity\_step4.submit**
+
+\#!/bin/sh
+\#SBATCH --job-name=Trinity\_Step4
+\#SBATCH --nodes=1
+\#SBATCH --ntasks-per-node=8
+\#SBATCH --time=168:00:00
+\#SBATCH --mem=100gb
+\#SBATCH --output=Trinity\_Step4.%J.out
+\#SBATCH --error=Trinity\_Step4.%J.err
+
+
+
+| |
+|-------------------------------------------------------------|
+| module load bowtie/1.0.0 samtools/0.1 trinity/r2014-04-13p1 |
+
+Trinity --seqType fq --JM 100G --left input\_reads\_pair\_1.fastq
+--right input\_reads\_pair\_2.fastq --SS\_lib\_type FR --output
+trinity\_out/ --CPU $SLURM\_NTASKS\_PER\_NODE
+
+
+
+**<span style="color: rgb(0,0,0);">Trinity Output</span>**
+
+<span style="color: rgb(0,0,0);">Trinity outputs number of files in its
+*trinity\_out/* output directory after each executed step. The output
+file *Trinity.fasta* is the final Trinity output that contains the
+assembled transcripts.</span>
+
+<span style="color: rgb(0,0,0);">
+</span>
+
+Memory Requirement
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-warning confluence-information-macro-icon"></span>
+
+<span style="color: rgb(0,0,0);">The Inchworm (step 1) and Chrysalis
+(step 2) steps can be memory intensive. A basic recommendation is to
+have **1GB of RAM per 1M **</span><span
+style="color: rgb(0,0,0);">**\~76 base Illumina paired-end
+reads**.</span>
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[cb\_trinity\_module.xsl](attachments/8193287/8127536.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193287/8127537.xml)
+(application/octet-stream)
+
+Document generated by Confluence on Oct 24, 2018 14:54
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/bioinformatics_tools/de_novo_assembly_tools/velvet/_index.md b/content/guides/running_applications/bioinformatics_tools/de_novo_assembly_tools/velvet/_index.md
new file mode 100644
index 00000000..061878af
--- /dev/null
+++ b/content/guides/running_applications/bioinformatics_tools/de_novo_assembly_tools/velvet/_index.md
@@ -0,0 +1,173 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Running Applications](Running-Applications_7471153.html)
+5. [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
+6. [De Novo Assembly Tools](De-Novo-Assembly-Tools_8193280.html)
+
+<span id="title-text"> HCC-DOCS : Velvet </span>
+================================================
+
+Created by <span class="author"> Adam Caprez</span> on Sep 04, 2014
+
+| Name | Version | Resource | Additional Information |
+|--------|---------|----------|-----------------------------------------------------------------------------------------------------|
+| velvet | 1.2 | Tusker | Velvet is compiled with CATEGORIES=4, MAXKMERLENGTH=64, OPENMP=1, LONGSEQUENCES=1 and BIGASSEMBLY=1 |
+
+| | | | |
+|--------|-----|-------|-----------------------------------------------------------------------------------------------------|
+| velvet | 1.2 | Crane | Velvet is compiled with CATEGORIES=4, MAXKMERLENGTH=64, OPENMP=1, LONGSEQUENCES=1 and BIGASSEMBLY=1 |
+
+
+
+Velvet
+(<a href="http://www.ebi.ac.uk/~zerbino/velvet/" class="external-link">http://www.ebi.ac.uk/~zerbino/velvet/</a>)
+is a general sequence assembler designed to produce assembly from short,
+as well as long reads. Running Velvet consists of a sequence of two
+commands: **velveth** and **velvetg**. **Velveth** produces a hash table
+of k-mers, while **velvetg** constructs the genome assembly. The k-mer
+length, also known as hash length corresponds to the length, in base
+pairs, of the words of the reads being hashed.
+
+Velvet has a lot of parameters that can be found in its manual:
+<a href="https://www.ebi.ac.uk/~zerbino/velvet/Manual.pdf" class="external-link">https://www.ebi.ac.uk/~zerbino/velvet/Manual.pdf</a>.
+However, the k-mer value is crucial in obtaining optimal assemblies.
+Higher k-mer values increase the specificity, and lower k-mer values
+increase the sensitivity.
+
+Velvet supports multiple file formats: **fasta**, **fastq**,
+**fasta.gz**, **fastq.gz**, **sam**, **bam**, **eland**,
+**gerald. **Velvet also supports different read categories for different
+sequencing technologies and libraries: **short**, **shortPaired**,
+**short2**, **shortPaired2**, **long**, **longPaired**.
+
+Each step of Velvet (**velveth** and **velvetg**) may be run as its own
+job. This following pages describe how to run Velvet in this manner
+under the SLURM scheduler on HCC and provide example submit scripts:
+
+
+
+**Useful Information**
+
+In order to test the VELVET (velvet/1.2) performance on Tusker, we used
+three paired-end input fastq files: **small\_1.fastq**,
+**small\_2.fastq**, **medium\_1.fastq**, **medium\_2.fastq**,
+**large\_1.fastq**, **large\_2.fastq**. Some statistics about the input
+files and the time and memory resources required for VELVET are shown on
+the table below:
+
+
+
+**total \# of sequences**
+
+**total \# of bases**
+
+**total size in MB**
+
+**VELVETH required time**
+
+**VELVETH required memory**
+
+**VELVETG required time**
+
+**VELVETG required memory**
+
+\# of used CPUs
+
+**small\_1.fastq**
+
+50,121
+
+2,506,050
+
+8.010 MB
+
+\~ 0.02 minutes
+
+\~ 0.3 GB
+
+\~ 0.08 minutes
+
+\~ 0.2 GB
+
+8
+
+**small\_2.fastq**
+
+50,121
+
+2,506,050
+
+8.010 MB
+
+**medium\_1.fastq**
+
+786,742
+
+59,792,392
+
+152 MB
+
+\~ 0.4 minutes
+
+\~ 1.5 GB
+
+\~ 0.8 minutes
+
+\~ 0.9 GB
+
+8
+
+**medium\_2.fastq**
+
+786,742
+
+59,792,392
+
+152 MB
+
+**large\_1.fastq**
+
+10,174,715
+
+1,027,646,215
+
+3,376 MB
+
+\~ 7 minutes
+
+\~ 23 GB
+
+\~ 45 minutes
+
+\~ 51 GB
+
+8
+
+**large\_2.fastq**
+
+10,174,715
+
+1,027,646,215
+
+3,376 MB
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193281/8127519.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_velvet\_version.xsl](attachments/8193281/8127520.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193281/8127521.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_velvet\_version.xsl](attachments/8193281/8127522.xsl)
+(application/octet-stream)
+
+Document generated by Confluence on Oct 24, 2018 14:54
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/bioinformatics_tools/de_novo_assembly_tools/velvet/running_velvet_with_paired_end_data.md b/content/guides/running_applications/bioinformatics_tools/de_novo_assembly_tools/velvet/running_velvet_with_paired_end_data.md
new file mode 100644
index 00000000..697c63f2
--- /dev/null
+++ b/content/guides/running_applications/bioinformatics_tools/de_novo_assembly_tools/velvet/running_velvet_with_paired_end_data.md
@@ -0,0 +1,1331 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Running Applications](Running-Applications_7471153.html)
+5. [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
+6. [De Novo Assembly Tools](De-Novo-Assembly-Tools_8193280.html)
+7. [Velvet](Velvet_8193281.html)
+
+<span id="title-text"> HCC-DOCS : Running Velvet with Paired-End Data </span>
+=============================================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified by
+<span class="editor"> Natasha Pavlovikj</span> on Dec 12, 2016
+
+**Running Velvet with Paired-End long fastq data with k-mer = 43, 8 CPUs
+and 100GB of RAM**
+
+The first step of running Velvet is to run **velveth**:
+
+**velveth.submit**
+
+\#!/bin/sh
+\#SBATCH --job-name=Velvet\_Velveth
+\#SBATCH --nodes=1
+\#SBATCH --ntasks-per-node=8
+\#SBATCH --time=168:00:00
+\#SBATCH --mem=100gb
+\#SBATCH --output=Velveth.%J.out
+\#SBATCH --error=Velveth.%J.err
+
+
+
+| |
+|------------------------|
+| module load velvet/1.2 |
+
+export OMP\_NUM\_THREADS=$SLURM\_NTASKS\_PER\_NODE
+
+velveth output\_directory/ 43 -fastq -longPaired -separate
+input\_reads\_pair\_1.fastq input\_reads\_pair\_2.fastq
+
+<span style="line-height: 1.4285715;">After
+running </span>**velveth**<span style="line-height: 1.4285715;">, the
+next step is to run </span>**velvetg**<span
+style="line-height: 1.4285715;"> on the *output\_directory/* and files
+generated from </span>**velveth:**
+
+**velvetg.submit**
+
+\#!/bin/sh
+\#SBATCH --job-name=Velvet\_Velvetg
+\#SBATCH --nodes=1
+\#SBATCH --ntasks-per-node=8
+\#SBATCH --time=168:00:00
+\#SBATCH --mem=100gb
+\#SBATCH --output=Velvetg.%J.out
+\#SBATCH --error=Velvetg.%J.err
+
+
+
+| |
+|------------------------|
+| module load velvet/1.2 |
+
+export OMP\_NUM\_THREADS=$SLURM\_NTASKS\_PER\_NODE
+
+velvetg output\_directory/ -min\_contig\_lgth 200
+
+Both **velveth** and **velvetg** are multi-threaded.
+
+
+
+**Check *output\_directory/* after velveth:**
+
+**Check Output Directory After Velveth**
+
+``` syntaxhighlighter-pre
+[<username>@login.tusker ~]$ ls output_directory/
+Log Roadmaps Sequences
+```
+
+************Check ***output\_directory/*** after velvetg:************
+
+**Check Output Directory After Velvetg**
+
+``` syntaxhighlighter-pre
+[<username>@login.tusker ~]$ ls output_directory/
+contigs.fa Graph LastGraph Log PreGraph Roadmaps Sequences stats.txt
+```
+
+The output fasta file *contigs.fa* is the final Velvet output that
+contains the assembled contigs. More information about the output files
+is provided in the Velvet manual.
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[cb\_velvet\_module.xsl](attachments/8193283/8127525.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193283/9863458.xml)
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+[tusker\_modules.xml](attachments/8193283/30444590.xml)
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193283/30444843.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193283/30444945.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193283/30445009.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193283/30445115.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193283/30445217.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193283/30445444.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193283/30445547.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193283/30445659.xml)
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193283/30445974.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193283/30446043.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193283/30446189.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193283/30446295.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193283/30446402.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193283/30446594.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193283/30446653.xml)
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193283/30446830.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193283/30446932.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193283/30447094.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193283/30447156.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193283/30447265.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193283/30447489.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193283/30447593.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193283/30447666.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193283/30447766.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193283/30448001.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193283/30448101.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193283/30448307.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193283/30448450.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193283/30448677.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193283/30448780.xml)
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193283/30448887.xml)
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193283/30448995.xml)
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193283/33685727.xml)
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193283/33686081.xml)
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193283/33686185.xml)
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193283/33686324.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193283/33687860.xml)
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193283/33688469.xml)
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193283/33689793.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193283/33690013.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193283/35324053.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193283/35324163.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193283/35324633.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193283/35324923.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193283/35325655.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193283/35325768.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193283/35326755.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193283/9863422.xml)
+(application/octet-stream)
+
+Document generated by Confluence on Oct 24, 2018 14:54
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/bioinformatics_tools/de_novo_assembly_tools/velvet/running_velvet_with_single_end_and_paired_end_data.md b/content/guides/running_applications/bioinformatics_tools/de_novo_assembly_tools/velvet/running_velvet_with_single_end_and_paired_end_data.md
new file mode 100644
index 00000000..a35750e5
--- /dev/null
+++ b/content/guides/running_applications/bioinformatics_tools/de_novo_assembly_tools/velvet/running_velvet_with_single_end_and_paired_end_data.md
@@ -0,0 +1,108 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Running Applications](Running-Applications_7471153.html)
+5. [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
+6. [De Novo Assembly Tools](De-Novo-Assembly-Tools_8193280.html)
+7. [Velvet](Velvet_8193281.html)
+
+<span id="title-text"> HCC-DOCS : Running Velvet with Single-End and Paired-End Data </span>
+============================================================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified by
+<span class="editor"> Natasha Pavlovikj</span> on Dec 12, 2016
+
+**Running Velvet with Single-End and Paired-End short fasta data with
+k-mer = 51, 8 CPUs and 100GB of RAM**
+
+The first step of running Velvet is to run** **velveth**:**
+
+**velveth.submit**
+
+\#!/bin/sh
+\#SBATCH --job-name=Velvet\_Velveth
+\#SBATCH --nodes=1
+\#SBATCH --ntasks-per-node=8
+\#SBATCH --time=168:00:00
+\#SBATCH --mem=100gb
+\#SBATCH --output=Velveth.%J.out
+\#SBATCH --error=Velveth.%J.err
+
+
+
+| |
+|------------------------|
+| module load velvet/1.2 |
+
+export OMP\_NUM\_THREADS=$SLURM\_NTASKS\_PER\_NODE
+
+velveth output\_directory/ 51 -fasta -short input\_reads.fasta -fasta
+-shortPaired2 -separate input\_reads\_pair\_1.fasta
+input\_reads\_pair\_2.fasta
+
+<span style="line-height: 1.4285715;">After
+running </span>**velveth**<span style="line-height: 1.4285715;">, the
+next step is to run </span>**velvetg**<span
+style="line-height: 1.4285715;"> on the *output\_directory/* and files
+generated from </span>**velveth:**
+
+**velvetg.submit**
+
+\#!/bin/sh
+\#SBATCH --job-name=Velvet\_Velvetg
+\#SBATCH --nodes=1
+\#SBATCH --ntasks-per-node=8
+\#SBATCH --time=168:00:00
+\#SBATCH --mem=100gb
+\#SBATCH --output=Velvetg.%J.out
+\#SBATCH --error=Velvetg.%J.err
+
+
+
+| |
+|------------------------|
+| module load velvet/1.2 |
+
+export OMP\_NUM\_THREADS=$SLURM\_NTASKS\_PER\_NODE
+
+velvetg output\_directory/ -min\_contig\_lgth 200
+
+Both **velveth** and **velvetg** are multi-threaded.
+
+
+
+**Check *output\_directory/* after velveth:**
+
+**Check Output Directory After Velveth**
+
+``` syntaxhighlighter-pre
+[<username>@login.tusker ~]$ ls output_directory/
+Log Roadmaps Sequences
+```
+
+************Check *output\_directory/* after velvetg:************
+
+**Check Output Directory After Velvetg**
+
+``` syntaxhighlighter-pre
+[<username>@login.tusker ~]$ ls output_directory/
+contigs.fa Graph LastGraph Log PreGraph Roadmaps Sequences stats.txt
+```
+
+The output fasta file *contigs.fa* is the final Velvet output that
+contains the assembled contigs. More information about the output files
+is provided in the Velvet manual.
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[cb\_velvet\_module.xsl](attachments/8193284/8127527.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193284/8127528.xml)
+(application/octet-stream)
+
+Document generated by Confluence on Oct 24, 2018 14:54
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/bioinformatics_tools/de_novo_assembly_tools/velvet/running_velvet_with_single_end_data.md b/content/guides/running_applications/bioinformatics_tools/de_novo_assembly_tools/velvet/running_velvet_with_single_end_data.md
new file mode 100644
index 00000000..f545bfa7
--- /dev/null
+++ b/content/guides/running_applications/bioinformatics_tools/de_novo_assembly_tools/velvet/running_velvet_with_single_end_data.md
@@ -0,0 +1,104 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Running Applications](Running-Applications_7471153.html)
+5. [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
+6. [De Novo Assembly Tools](De-Novo-Assembly-Tools_8193280.html)
+7. [Velvet](Velvet_8193281.html)
+
+<span id="title-text"> HCC-DOCS : Running Velvet with Single-End Data </span>
+=============================================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified by
+<span class="editor"> Natasha Pavlovikj</span> on Dec 12, 2016
+
+**Running Velvet with Single-End short fasta data with k-mer = 31, 8
+CPUs and 100GB of RAM**
+
+The first step of running Velvet is to run **velveth**:
+
+**velveth.submit**
+
+\#!/bin/sh
+\#SBATCH --job-name=Velvet\_Velveth
+\#SBATCH --nodes=1
+\#SBATCH --ntasks-per-node=8
+\#SBATCH --time=168:00:00
+\#SBATCH --mem=100gb
+\#SBATCH --output=Velveth.%J.out
+\#SBATCH --error=Velveth.%J.err
+
+
+
+| |
+|------------------------|
+| module load velvet/1.2 |
+
+export OMP\_NUM\_THREADS=$SLURM\_NTASKS\_PER\_NODE
+
+velveth output\_directory/ 31 -fasta -short input\_reads.fasta
+
+After running **velveth**, the next step is to run **velvetg** on the
+*output\_directory/* and files generated from **velveth:**
+
+**velvetg.submit**
+
+\#!/bin/sh
+\#SBATCH --job-name=Velvet\_Velvetg
+\#SBATCH --nodes=1
+\#SBATCH --ntasks-per-node=8
+\#SBATCH --time=168:00:00
+\#SBATCH --mem=100gb
+\#SBATCH --output=Velvetg.%J.out
+\#SBATCH --error=Velvetg.%J.err
+
+
+
+| |
+|------------------------|
+| module load velvet/1.2 |
+
+export OMP\_NUM\_THREADS=$SLURM\_NTASKS\_PER\_NODE
+
+velvetg output\_directory/ -min\_contig\_lgth 200
+
+Both **velveth** and **velvetg** are multi-threaded.
+
+****
+****
+
+****Check *output\_directory/* after velveth:****
+
+**Check Output Directory After Velveth**
+
+``` syntaxhighlighter-pre
+[<username>@login.tusker ~]$ ls output_directory/
+Log Roadmaps Sequences
+```
+
+************Check *output\_directory/* after velvetg:************
+
+**Check Output Directory After Velvetg**
+
+``` syntaxhighlighter-pre
+[<username>@login.tusker ~]$ ls output_directory/
+contigs.fa Graph LastGraph Log PreGraph Roadmaps Sequences stats.txt
+```
+
+The output fasta file *contigs.fa* is the final Velvet output that
+contains the assembled contigs. More information about the output files
+is provided in the Velvet manual.
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[cb\_velvet\_module.xsl](attachments/8193282/8127523.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193282/8127524.xml)
+(application/octet-stream)
+
+Document generated by Confluence on Oct 24, 2018 14:54
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/bioinformatics_tools/downloading_sra_data_from_ncbi.md b/content/guides/running_applications/bioinformatics_tools/downloading_sra_data_from_ncbi.md
new file mode 100644
index 00000000..f506a848
--- /dev/null
+++ b/content/guides/running_applications/bioinformatics_tools/downloading_sra_data_from_ncbi.md
@@ -0,0 +1,89 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Running Applications](Running-Applications_7471153.html)
+5. [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
+
+<span id="title-text"> HCC-DOCS : Downloading SRA data from NCBI </span>
+========================================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified by
+<span class="editor"> Natasha Pavlovikj</span> on Apr 16, 2018
+
+One way to download high-volume data from NCBI is to use command line
+utilities, such as **wget**, **ftp** or Aspera Connect **ascp**
+plugin.
+The Aspera Connect plugin is commonly used high-performance transfer
+plugin that provides the best transfer speed.
+
+In order to use this plugin on the HCC supercomputers, you need to
+download the latest Linux version from the Asera web site
+(<a href="http://downloads.asperasoft.com/en/downloads/8?list" class="external-link">http://downloads.asperasoft.com/en/downloads/8?list</a>).
+The current Linux version is 3.7.4, and after you login to HCC and open
+a command line interface, just type:
+
+**Download Aspera Plugin**
+
+``` syntaxhighlighter-pre
+[<username>@login.tusker ~]$ wget https://download.asperasoft.com/download/sw/connect/3.7.4/aspera-connect-3.7.4.147727-linux-64.tar.gz
+[<username>@login.tusker ~]$ tar xvf aspera-connect-3.7.4.147727-linux-64.tar.gz
+```
+
+This will download and extract the plugin in your current
+directory. After that, you need to install the plugin by typing:
+
+**Install Aspera Plugin**
+
+``` syntaxhighlighter-pre
+[<username>@login.tusker ~]$ sh aspera-connect-3.7.4.147727-linux-64.sh
+```
+
+This command will install the plugin in **.aspera/** directory in your
+**home/** directory
+(*/home/<groupname>/<username>/.aspera/*).
+
+The basic usage of the Aspera plugin is:
+
+**Basic Usage of Aspera Plugin**
+
+``` syntaxhighlighter-pre
+[<username>@login.tusker ~]$ ~/.aspera/connect/bin/ascp -i ~/.aspera/connect/etc/asperaweb_id_dsa.openssh -k 1 -T -l <max_download_rate_in_Mbps>m anonftp@ftp.ncbi.nlm.nih.gov:/<files_to_transfer> <local_work_output_directory>
+```
+
+where **-k 1** enables resume of partial transfers, **-T** disables
+encryption for maximum throughput, and **-l** sets the transfer rate.
+
+**<files\_to\_transfer>** mentioned in the basic usage of Aspera
+plugin has a specifically defined pattern that needs to be followed:
+
+**<files\_to\_transfer>**
+
+``` syntaxhighlighter-pre
+<files_to_transfer> = /sra/sra-instant/reads/ByRun/sra/SRR|ERR|DRR/<first_6_characters_of_accession>/<accession>/<accession>.sra
+```
+
+where **SRR\|ERR\|DRR** should be either **SRR**, **ERR **or **DRR** and
+should match the prefix of the target **.sra** file.
+
+More **ascp** options can be seen by using:
+
+**Additional ASCP Options**
+
+``` syntaxhighlighter-pre
+[<username>@login.tusker ~]$ ascp --help
+```
+
+
+Finally, if you want to download the **SRR304976** file from NCBI in
+your work **data/** directory with downloading speed of **1000 Mbps**,
+you use:
+
+**ASCP Command Run**
+
+``` syntaxhighlighter-pre
+[<username>@login.tusker ~]$ ~/.aspera/connect/bin/ascp -i ~/.aspera/connect/etc/asperaweb_id_dsa.openssh -k 1 -T -l 1000m anonftp@ftp.ncbi.nlm.nih.gov:/sra/sra-instant/reads/ByRun/sra/SRR/SRR304/SRR304976/SRR304976.sra /work/<groupname>/<username>/data/
+```
+
+Document generated by Confluence on Oct 24, 2018 14:54
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/bioinformatics_tools/pre_processing_tools/_index.md b/content/guides/running_applications/bioinformatics_tools/pre_processing_tools/_index.md
new file mode 100644
index 00000000..1f7da760
--- /dev/null
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@@ -0,0 +1,16 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Running Applications](Running-Applications_7471153.html)
+5. [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
+
+<span id="title-text"> HCC-DOCS : Pre-Processing Tools </span>
+==============================================================
+
+Created by <span class="author"> Adam Caprez</span> on Sep 04, 2014
+
+
+
+Document generated by Confluence on Oct 24, 2018 14:54
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/bioinformatics_tools/pre_processing_tools/cutadapt.md b/content/guides/running_applications/bioinformatics_tools/pre_processing_tools/cutadapt.md
new file mode 100644
index 00000000..81f48a9c
--- /dev/null
+++ b/content/guides/running_applications/bioinformatics_tools/pre_processing_tools/cutadapt.md
@@ -0,0 +1,121 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Running Applications](Running-Applications_7471153.html)
+5. [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
+6. [Pre-Processing Tools](Pre-Processing-Tools_8193298.html)
+
+<span id="title-text"> HCC-DOCS : Cutadapt </span>
+==================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified by
+<span class="editor"> Natasha Pavlovikj</span> on Dec 12, 2016
+
+| Name | Version | Resource |
+|----------|---------|----------|
+| cutadapt | 1.4 | Tusker |
+
+| | | |
+|----------|-----|-------|
+| cutadapt | 1.4 | Crane |
+
+
+
+Cutadapt
+(<a href="https://code.google.com/p/cutadapt/" class="external-link">https://code.google.com/p/cutadapt/</a>)
+is a tool for removing adapter sequences from DNA sequencing data.
+Although most of the adapters are located at the 3' end of the
+sequencing read, Cutadapt allows multiple adapter removal from both 3'
+and 5' ends.
+
+The basic usage of Cutadapt is:
+
+**General Cutadapt Usage**
+
+``` syntaxhighlighter-pre
+cutadapt [-a|-b|-g] <adapter_sequence> input_reads.[fasta|fastq] > output_reads.[fasta|fastq]
+```
+
+where **<adapter\_sequence>** is the nucleotide sequence of the
+actual adapter, i**nput\_reads.\[fasta\|fastq\]** is the input file with
+sequencing data in fasta/fastq format, and respectively,
+**output\_reads.\[fasta\|fastq\]** is the final trimmed file in
+fasta/fastq format. The option **-a** allows removing of an adapter from
+the 3' end of the sequencing read. The option **-b** removes adapters
+ligated to the 5' or 3' end. The option **-g** removes adapter sequences
+from the 5' end. These options can be used multiple times for different
+adapters.
+
+More information about the Cutadapt options can be found by typing:
+
+**Additional Cutadapt Options**
+
+``` syntaxhighlighter-pre
+[<username>@login.tusker~]$ cutadapt --help
+```
+
+Simple Cutadapt script that trims the adapter sequences **AGGCACACAGGG**
+and **TGAGACACGCA** from the 3' end and **AACCGGTT** from the 5' end of
+single-end fasta input file is shown below:
+
+**cutadapt.submit**
+
+\#!/bin/sh
+\#SBATCH --job-name=Cutadapt
+\#SBATCH --nodes=1
+\#SBATCH --ntasks-per-node=1
+\#SBATCH --time=168:00:00
+\#SBATCH --mem=30gb
+\#SBATCH --output=Cutadapt.%J.out
+\#SBATCH --error=Cutadapt.%J.err
+
+
+
+| |
+|-------------------------------------|
+| module load python/2.7 cutadapt/1.4 |
+
+cutadapt -a AGGCACACAGGG -a TGAGACACGCA -g AACCGGTT input\_reads.fasta
+> output\_reads.fasta
+
+Cutadapt is single threaded program, and therefore **\#SBATCH
+--nodes=1** and **\#SBATCH --ntasks-per-node=1**. Cutadapt allows
+paired-end trimming where each pair is trimmed separately in a single
+pass:
+
+**Cutadapt Usage for Paired-End Reads**
+
+``` syntaxhighlighter-pre
+cutadapt -a ADAPTER_PAIR_1 input_reads_pair_1.fastq > output_reads_pair_1.fastq
+cutadapt -a ADAPTER_PAIR_2 input_reads_pair_2.fastq > output_reads_pair_2.fastq
+```
+
+
+
+**Cutadapt Output**
+
+Beside the fasta/fastq file of reads with removed adapter sequences,
+Cutadapt also outputs useful statistics per adapter sequence.
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[cb\_cutadapt\_module.xsl](attachments/8193303/8127586.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_cutadapt\_version.xsl](attachments/8193303/8127587.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193303/8127588.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_cutadapt\_version.xsl](attachments/8193303/8127589.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193303/8127590.xml)
+(application/octet-stream)
+
+Document generated by Confluence on Oct 24, 2018 14:54
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/bioinformatics_tools/pre_processing_tools/prinseq.md b/content/guides/running_applications/bioinformatics_tools/pre_processing_tools/prinseq.md
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index 00000000..f000410b
--- /dev/null
+++ b/content/guides/running_applications/bioinformatics_tools/pre_processing_tools/prinseq.md
@@ -0,0 +1,152 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Running Applications](Running-Applications_7471153.html)
+5. [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
+6. [Pre-Processing Tools](Pre-Processing-Tools_8193298.html)
+
+<span id="title-text"> HCC-DOCS : PRINSEQ </span>
+=================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified by
+<span class="editor"> Natasha Pavlovikj</span> on Dec 12, 2016
+
+| Name | Version | Resource |
+|--------------|---------|----------|
+| prinseq-lite | 0.20 | Crane |
+
+
+
+PRINSEQ (PReprocessing and INformation of SEQuence data)
+(<a href="http://prinseq.sourceforge.net/" class="external-link">http://prinseq.sourceforge.net/</a>)
+is a tool used for filtering, formatting or trimming genome and
+metagenomic sequence data in fasta/fastq format. Moreover, PRINSEQ
+generates summary statistics of sequence and quality data.
+
+More information about the PRINSEQ program can be shown with:
+
+**Additional PRINSEQ Options**
+
+``` syntaxhighlighter-pre
+[<username>@login.crane ~]$ prinseq-lite.pl --help
+```
+
+**
+**
+
+**PRINSEQ script for single-end fasta data**
+
+The basic usage of PRINSEQ for single-end data is:
+
+**General PRINSEQ Usage for Single-End Data**
+
+``` syntaxhighlighter-pre
+prinseq-lite.pl [-fasta|-fastq] input_reads.[fasta|fastq] -out_format [1|2|3|4|5] [options]
+```
+
+where **input\_reads.\[fasta\|fastq\]** is an input file of sequence
+data in fasta/fastq format, and **options** are additional parameters
+that can be found in the PRINSEQ manual:
+<a href="http://prinseq.sourceforge.net/manual.html" class="external-link">http://prinseq.sourceforge.net/manual.html</a>.
+The output format (**-out\_format**) can be **1 **(fasta only),
+**2 **(fasta and qual), **3 **(fastq), **4 **(fastq and input fasta),
+and **5 **(fastq, fasta and qual).
+
+Simple PRINSEQ SLURM script for single-end fasta data and fasta output
+format is shown below:
+
+**prinseq\_single\_end.submit**
+
+\#!/bin/sh
+\#SBATCH --job-name=PRINSEQ
+\#SBATCH --nodes=1
+\#SBATCH --ntasks-per-node=1
+\#SBATCH --time=168:00:00
+\#SBATCH --mem=20gb
+\#SBATCH --output=PRINSEQ\_single.%J.out
+\#SBATCH --error=PRINSEQ\_single.%J.err
+
+
+
+| |
+|-------------------------------|
+| module load prinseq-lite/0.20 |
+
+prinseq-lite.pl -fasta input\_reads.fasta -out\_format 1
+
+PRINSEQ is single threaded program, and therefore both **\#SBATCH
+--nodes** and **\#SBATCH --ntasks-per-node** are set to **1**.
+
+
+
+**PRINSEQ script for paired-end fastq data**
+
+The basic usage of PRINSEQ for paired-end data is:
+
+**General PRINSEQ Usage for Paired-End Data**
+
+``` syntaxhighlighter-pre
+prinseq-lite.pl [-fasta|-fastq] input_reads_pair_1.[fasta|fastq] [-fasta2|-fastq2] input_reads_pair_2.[fasta|fastq] -out_format [1|2|3|4|5] [options]
+```
+
+where **input\_reads\_pair\_1.\[fasta\|fastq\]**
+and ****input\_reads\_pair\_2.\[fasta\|fastq\]**** are pair 1 and pair 2
+of the input files of sequence data in fasta/fastq format,
+and **options** are additional parameters that can be found in the
+PRINSEQ
+manual: <a href="http://prinseq.sourceforge.net/manual.html" class="external-link">http://prinseq.sourceforge.net/manual.html</a>.
+The output format (**-out\_format**) can be **1 **(fasta only),
+**2 **(fasta and qual), **3 **(fastq), **4 **(fastq and input fasta),
+and **5 **(fastq, fasta and qual).
+
+Simple PRINSEQ SLURM script for paired-end fastq data and fastq output
+format is shown below:
+
+**prinseq\_paired\_end.submit**
+
+\#!/bin/sh
+\#SBATCH --job-name=PRINSEQ
+\#SBATCH --nodes=1
+\#SBATCH --ntasks-per-node=1
+\#SBATCH --time=168:00:00
+\#SBATCH --mem=20gb
+\#SBATCH --output=PRINSEQ\_paired.%J.out
+\#SBATCH --error=PRINSEQ\_paired.%J.err
+
+
+
+| |
+|-------------------------------|
+| module load prinseq-lite/0.20 |
+
+prinseq-lite.pl -fastq input\_reads\_pair\_1.fastq -fastq2
+input\_reads\_pair\_2.fastq -out\_format 3
+
+PRINSEQ is single threaded program, and therefore both **\#SBATCH
+--nodes** and **\#SBATCH --ntasks-per-node** are set to **1**.
+
+**
+**
+
+**PRINSEQ Output**
+
+PRINSEQ gives statistics about the input and filtered sequences, and
+also outputs single-end or paired-end files of sequences filtered by
+specified parameters.
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[cb\_prinseq\_module.xsl](attachments/8193299/8127572.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193299/8127573.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_prinseq\_version.xsl](attachments/8193299/8127574.xsl)
+(application/octet-stream)
+
+Document generated by Confluence on Oct 24, 2018 14:54
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/bioinformatics_tools/pre_processing_tools/scythe.md b/content/guides/running_applications/bioinformatics_tools/pre_processing_tools/scythe.md
new file mode 100644
index 00000000..90bedd17
--- /dev/null
+++ b/content/guides/running_applications/bioinformatics_tools/pre_processing_tools/scythe.md
@@ -0,0 +1,193 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Running Applications](Running-Applications_7471153.html)
+5. [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
+6. [Pre-Processing Tools](Pre-Processing-Tools_8193298.html)
+
+<span id="title-text"> HCC-DOCS : Scythe </span>
+================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified by
+<span class="editor"> Natasha Pavlovikj</span> on Dec 12, 2016
+
+| Name | Version | Resource |
+|--------|---------|----------|
+| scythe | 0.991 | Tusker |
+
+
+
+Scythe
+(<a href="https://github.com/vsbuffalo/scythe" class="external-link">https://github.com/vsbuffalo/scythe</a>)
+is a 3' end adapter trimmer that uses a Naive Bayesian approach to
+classify contaminant substrings in sequence reads. 3' ends often include
+poor quality bases which need to be removed prior the quality-based
+trimming, mapping, assemblies, and further analysis.
+
+The basic usage of Scythe is:
+
+**General Scythe Usage**
+
+``` syntaxhighlighter-pre
+scythe -a adapter_file.fasta input_reads.fastq -o output_reads.fastq
+```
+
+where **adapter\_file.fasta** is a fasta input file of the adapter
+sequences that need to be removed from the 3' end of the sequence data,
+and **input\_reads.fastq** is the input sequencing data in fastq format.
+The file **output\_reads.fastq** contains the sequencing reads with
+removed adapters. If the adapter sequences are unknown, Scythe by itself
+provides two adapter sequences that can be used with the **-a**
+option: **illumina\_adapters.fa** and **truseq\_adapters.fasta**.
+
+More information about Scythe can found by typing:
+
+**Additional Scythe Options**
+
+``` syntaxhighlighter-pre
+[<username>@login.tusker ~]$ scythe --help
+```
+
+Simple Scythe script that uses the **illumina\_adapters.fa** file and
+**input\_reads.fastq** for Tusker is shown below:
+
+**scythe.submit**
+
+\#!/bin/sh
+\#SBATCH --job-name=Scythe
+\#SBATCH --nodes=1
+\#SBATCH --ntasks-per-node=1
+\#SBATCH --time=168:00:00
+\#SBATCH --mem=20gb
+\#SBATCH --output=Scythe.%J.out
+\#SBATCH --error=Scythe.%J.err
+
+
+
+| |
+|--------------------------|
+| module load scythe/0.991 |
+
+scythe -a $SCYTHE\_HOME/illumina\_adapters.fa input\_reads.fastq -o
+output\_reads.fastq
+
+Scythe is single threaded program, and therefore both **\#SBATCH
+--nodes** and **\#SBATCH --ntasks-per-node** are set to **1**. The two
+adapter sequences provided by Scythe are stored in **$SCYTHE\_HOME**.
+Hence, to access the illumina adapter file
+use: **$SCYTHE\_HOME/illumina\_adapters.fa**, and to access the TruSeq
+file use:** $SCYTHE\_HOME/**truseq\_adapters.fasta****.
+
+**
+**
+
+**Scythe Output**
+
+Scythe returns fastq file of reads with removed adapter sequences.
+
+
+
+**Useful Information**
+
+In order to test the SCYTHE (scythe/0.991) performance on Tusker, we
+used three paired-end input fastq files: **small\_1.fastq**,
+**small\_2.fastq**, **medium\_1.fastq**, **medium\_2.fastq**,
+**large\_1.fastq, large\_2.fastq**. Some statistics about the input
+files and the time and memory resources required for SCYTHE are shown on
+the table below:
+
+<table style="width:100%;">
+<colgroup>
+<col style="width: 14%" />
+<col style="width: 14%" />
+<col style="width: 14%" />
+<col style="width: 14%" />
+<col style="width: 14%" />
+<col style="width: 14%" />
+<col style="width: 14%" />
+</colgroup>
+<thead>
+<tr class="header">
+<th> </th>
+<th><p><strong>total # of sequences</strong></p></th>
+<th><p><strong>total # of bases</strong></p></th>
+<th><p><strong>total size in MB</strong></p></th>
+<th><p><strong>required time</strong></p></th>
+<th><p><strong>required memory</strong></p></th>
+<th># of used CPUs</th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td><p><strong>small_1.fastq</strong></p></td>
+<td><p>50,121</p></td>
+<td><p>2,506,050</p></td>
+<td><p>8.010 MB</p></td>
+<td><p>~ 0.04 minutes</p></td>
+<td><span>~ 0.014 GB</span></td>
+<td>1</td>
+</tr>
+<tr class="even">
+<td><p><strong>small_2.fastq</strong></p></td>
+<td><p>50,121</p></td>
+<td><p>2,506,050</p></td>
+<td><p>8.010 MB</p></td>
+<td><p>~ 0.04 minutes</p></td>
+<td><p>~ 0.014 GB</p></td>
+<td>1</td>
+</tr>
+<tr class="odd">
+<td><p><strong>medium_1.fastq</strong></p></td>
+<td><p>786,742</p></td>
+<td><p>59,792,392</p></td>
+<td><p>152 MB</p></td>
+<td><p>~ 1 minutes</p></td>
+<td><p><span>~ 0.2 GB</span></p></td>
+<td>1</td>
+</tr>
+<tr class="even">
+<td><p><strong>medium_2.fastq</strong></p></td>
+<td><p>786,742</p></td>
+<td><p>59,792,392</p></td>
+<td><p>152 MB</p></td>
+<td><p>~ 1 minutes</p></td>
+<td><p>~ 0.2 GB</p></td>
+<td>1</td>
+</tr>
+<tr class="odd">
+<td><p><strong>large_1.fastq</strong></p></td>
+<td><p>10,174,715</p></td>
+<td><p>1,027,646,215</p></td>
+<td><p>3,376 MB</p></td>
+<td>~ 13 minutes</td>
+<td><p>~ 3 GB</p></td>
+<td>1</td>
+</tr>
+<tr class="even">
+<td><p><strong>large_2.fastq</strong></p></td>
+<td><p>10,174,715</p></td>
+<td><p>1,027,646,215</p></td>
+<td><p>3,376 MB</p></td>
+<td>~ 17 minutes</td>
+<td><p>~ 6.5 GB</p></td>
+<td>1</td>
+</tr>
+</tbody>
+</table>
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[cb\_scythe\_module.xsl](attachments/8193301/8127578.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193301/8127579.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_scythe\_version.xsl](attachments/8193301/8127580.xsl)
+(application/octet-stream)
+
+Document generated by Confluence on Oct 24, 2018 14:54
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/bioinformatics_tools/pre_processing_tools/sickle.md b/content/guides/running_applications/bioinformatics_tools/pre_processing_tools/sickle.md
new file mode 100644
index 00000000..5894cab7
--- /dev/null
+++ b/content/guides/running_applications/bioinformatics_tools/pre_processing_tools/sickle.md
@@ -0,0 +1,251 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Running Applications](Running-Applications_7471153.html)
+5. [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
+6. [Pre-Processing Tools](Pre-Processing-Tools_8193298.html)
+
+<span id="title-text"> HCC-DOCS : Sickle </span>
+================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified by
+<span class="editor"> Natasha Pavlovikj</span> on Dec 12, 2016
+
+| Name | Version | Resource |
+|--------|---------|----------|
+| sickle | 1.2 | Tusker |
+
+| | | |
+|--------|-------|-------|
+| sickle | 1.210 | Crane |
+
+
+
+Sickle
+(<a href="https://github.com/najoshi/sickle" class="external-link">https://github.com/najoshi/sickle</a>)
+is a windowed adaptive trimming tools for fastq files. Beside sliding
+window, Sickle uses quality and length thresholds to determine and trim
+low quality bases at both 3' end and 5' end of the reads.
+
+Information about the Sickle command-line options can be shown by
+typing:
+
+**Additional Sickle Options**
+
+``` syntaxhighlighter-pre
+[<username>@login.tusker ~]$ sickle --help
+```
+
+Sickle is single threaded program.
+
+
+
+**Sickle for single-end reads**
+
+The basic usage of Sickle for single-end reads is:
+
+**General Sickle Usage for Single-End Reads**
+
+``` syntaxhighlighter-pre
+sickle se -t [solexa|illumina|sanger] -f input_reads.fastq -o output_reads_trimmed.fastq
+```
+
+where **input\_reads.fastq** is the input file of sequencing data in
+fastq format, and **output\_reads\_trimmed.fastq** is the trimmed output
+file. Another required option in **sickle se** is the **-t** option that
+based on the input data, accepts one of the following quality
+values: **solexa**, **illumina**, **sanger.**
+
+Simple SLURM Sickle script for Illumina single-end reads input file
+**input\_reads.fastq** is shown below:
+
+**sickle\_single.submit**
+
+\#!/bin/sh
+\#SBATCH --job-name=Sickle
+\#SBATCH --nodes=1
+\#SBATCH --ntasks-per-node=1
+\#SBATCH --time=168:00:00
+\#SBATCH --mem=30gb
+\#SBATCH --output=Sickle\_single.%J.out
+\#SBATCH --error=Sickle\_single.%J.err
+
+
+
+| |
+|------------------------|
+| module load sickle/1.2 |
+
+sickle se -t illumina -f input\_reads.fastq -o
+output\_reads\_trimmed.fastq
+
+
+
+**Sickle for paired-end reads**
+
+The basic usage of Sickle for paired-end reads is:
+
+**General Sickle Usage for Paired-End Reads**
+
+``` syntaxhighlighter-pre
+sickle pe -t [solexa|illumina|sanger] -f input_reads_pair_1.fastq -r input_reads_pair_2.fastq -o output_reads_trimmed_pair_1.fastq -p output_reads_trimmed_pair_2.fastq -s output_reads_trimmed_single.fastq
+```
+
+where **input\_reads\_pair\_1.fastq**
+and **input\_reads\_pair\_2.fastq** are the input fastq files of the
+sequencing data, and
+respectively, **output\_reads\_trimmed\_pair\_1.fastq**
+and **output\_reads\_trimmed\_pair\_2.fastq** are the trimmed output
+files. **Sickle pe** also
+prints **output\_reads\_trimmed\_single.fastq** file that contains reads
+that passed the filter in one pair, but not in the other read pair.
+Sickle supports three types of quality values: **solexa**, **illumina**,
+**sanger**, and this type must be specified using the **-t** option.
+
+Simple SLURM Sickle script for Sanger paired-end reads input
+files **input\_reads\_pair\_1.fastq**
+and ****input\_reads\_pair\_2.fastq**** is shown below:
+
+**sickle\_paired.submit**
+
+\#!/bin/sh
+\#SBATCH --job-name=Sickle
+\#SBATCH --nodes=1
+\#SBATCH --ntasks-per-node=1
+\#SBATCH --time=168:00:00
+\#SBATCH --mem=30gb
+\#SBATCH --output=Sickle\_paired.%J.out
+\#SBATCH --error=Sickle\_paired.%J.err
+
+
+
+| |
+|------------------------|
+| module load sickle/1.2 |
+
+sickle pe -t sanger -f input\_reads\_pair\_1.fastq -r
+input\_reads\_pair\_2.fastq -o output\_reads\_trimmed\_pair\_1.fastq -p
+output\_reads\_trimmed\_pair\_2.fastq -s
+output\_reads\_trimmed\_single.fastq
+
+
+
+**Sickle Output**
+
+Sickle returns fastq file of reads with trimmed low quality bases from
+both 3' and 5' ends. Sickle reduces the sequence length, while the
+number of sequences in the output file stays the same.
+
+
+
+**Useful Information**
+
+In order to test the SICKLE (sickle/1.2) performance on Tusker, we used
+three paired-end input fastq files: **small\_1.fastq**,
+**small\_2.fastq**, **medium\_1.fastq**, **medium\_2.fastq**,
+**large\_1.fastq**, **large\_2.fastq**. Some statistics about the input
+files and the time and memory resources required for SICKLE are shown on
+the table below:
+
+
+
+**total \# of sequences**
+
+**total \# of bases**
+
+**total size in MB**
+
+**required time**
+
+**required memory**
+
+\# of used CPUs
+
+**small\_1.fastq**
+
+50,121
+
+2,506,050
+
+8.010 MB
+
+\~ 0.03 minutes
+
+\~ 0.05 GB
+
+1
+
+**small\_2.fastq**
+
+50,121
+
+2,506,050
+
+8.010 MB
+
+**medium\_1.fastq**
+
+786,742
+
+59,792,392
+
+152 MB
+
+\~ 0.2 minutes
+
+\~ 0.7 GB
+
+1
+
+**medium\_2.fastq**
+
+786,742
+
+59,792,392
+
+152 MB
+
+**large\_1.fastq**
+
+10,174,715
+
+1,027,646,215
+
+3,376 MB
+
+\~ 3 minutes
+
+\~ 13 GB
+
+1
+
+**large\_2.fastq**
+
+10,174,715
+
+1,027,646,215
+
+3,376 MB
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[cb\_sickle\_module.xsl](attachments/8193302/8127581.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193302/8127582.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_sickle\_version.xsl](attachments/8193302/8127583.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193302/8127584.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_sickle\_version.xsl](attachments/8193302/8127585.xsl)
+(application/octet-stream)
+
+Document generated by Confluence on Oct 24, 2018 14:54
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/bioinformatics_tools/pre_processing_tools/tagcleaner.md b/content/guides/running_applications/bioinformatics_tools/pre_processing_tools/tagcleaner.md
new file mode 100644
index 00000000..f72576a2
--- /dev/null
+++ b/content/guides/running_applications/bioinformatics_tools/pre_processing_tools/tagcleaner.md
@@ -0,0 +1,104 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Running Applications](Running-Applications_7471153.html)
+5. [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
+6. [Pre-Processing Tools](Pre-Processing-Tools_8193298.html)
+
+<span id="title-text"> HCC-DOCS : TagCleaner </span>
+====================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified by
+<span class="editor"> Natasha Pavlovikj</span> on Dec 12, 2016
+
+| Name | Version | Resource |
+|------------|---------|----------|
+| tagcleaner | 0.16 | Crane |
+
+
+
+TagCleaner
+(<a href="http://tagcleaner.sourceforge.net/" class="external-link">http://tagcleaner.sourceforge.net/</a>)
+is a tool used to automatically detect and remove tag sequences from
+genomic and metagenomic sequence data. These additional tag sequences
+can contain deletions or insertions due to sequencing limitations.
+
+The basic usage of TagCleaner is:
+
+**General TagCleaner Usage**
+
+``` syntaxhighlighter-pre
+tagcleaner.pl [-fasta|-fastq] input_reads.[fasta|fastq] [-predict|-tag3|-tag5] [options]
+```
+
+where **input\_reads.\[fasta\|fastq\]** is an input file of sequence
+data in fasta/fastq format, and **options** are additional parameters
+that can be found in the TagCleaner
+manual: <a href="http://tagcleaner.sourceforge.net/manual.html" class="external-link">http://tagcleaner.sourceforge.net/manual.html</a>.
+Required parameter for TagCleaner is the tag sequence. If the tag
+sequence is unknown, then the **-predict** option will provide the
+predicted tag sequence to the user. If the tag sequence is known and is
+found at the 3' end of the read, then the option **-tag3
+<tag\_sequence>** is used. If the tag sequence is known and is
+found at the 5' end of the read, the the option **-tag5
+<tag\_sequence>** is used.
+
+More information about the TagCleaner options can be found by using:
+
+**Additional TagCleaner Options**
+
+``` syntaxhighlighter-pre
+[<username>@login.crane ~]$ tagcleaner.pl --help
+```
+
+Simple TagCleaner script for removing known 3' and 5' tag sequences
+(<span style="color: rgb(0,0,0);">NNNCCAAACACACCCAACACA
+and TGTGTTGGGTGTGTTTGGNNN respectively) is shown below:</span>
+
+**tagcleaner.submit**
+
+\#!/bin/sh
+\#SBATCH --job-name=TagCleaner
+\#SBATCH --nodes=1
+\#SBATCH --ntasks-per-node=1
+\#SBATCH --time=168:00:00
+\#SBATCH --mem=20gb
+\#SBATCH --output=TagCleaner.%J.out
+\#SBATCH --error=TagCleaner.%J.err
+
+
+
+| |
+|-----------------------------|
+| module load tagcleaner/0.16 |
+
+tagcleaner.pl -fasta input\_reads.fasta -tag3 NNNCCAAACACACCCAACACA
+-tag5 TGTGTTGGGTGTGTTTGGNNN
+
+TagCleaner is single threaded program, and therefore both **\#SBATCH
+--nodes** and** \#SBATCH --ntasks-per-node** are set to **1.**
+
+**
+**
+
+**TagCleaner Output**
+
+TagCleaner returns fasta or fastq file of reads with removed tag
+sequences.
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[cb\_tagcleaner\_module.xsl](attachments/8193300/8127575.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193300/8127576.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_tagcleaner\_version.xsl](attachments/8193300/8127577.xsl)
+(application/octet-stream)
+
+Document generated by Confluence on Oct 24, 2018 14:54
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/bioinformatics_tools/reference_based_assembly_tools/_index.md b/content/guides/running_applications/bioinformatics_tools/reference_based_assembly_tools/_index.md
new file mode 100644
index 00000000..742dec8d
--- /dev/null
+++ b/content/guides/running_applications/bioinformatics_tools/reference_based_assembly_tools/_index.md
@@ -0,0 +1,16 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Running Applications](Running-Applications_7471153.html)
+5. [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
+
+<span id="title-text"> HCC-DOCS : Reference-Based Assembly Tools </span>
+========================================================================
+
+Created by <span class="author"> Adam Caprez</span> on Sep 04, 2014
+
+
+
+Document generated by Confluence on Oct 24, 2018 14:54
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/bioinformatics_tools/reference_based_assembly_tools/cufflinks.md b/content/guides/running_applications/bioinformatics_tools/reference_based_assembly_tools/cufflinks.md
new file mode 100644
index 00000000..78b1abd8
--- /dev/null
+++ b/content/guides/running_applications/bioinformatics_tools/reference_based_assembly_tools/cufflinks.md
@@ -0,0 +1,2860 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Running Applications](Running-Applications_7471153.html)
+5. [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
+6. [Reference-Based Assembly
+ Tools](Reference-Based-Assembly-Tools_8193313.html)
+
+<span id="title-text"> HCC-DOCS : Cufflinks </span>
+===================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified by
+<span class="editor"> Natasha Pavlovikj</span> on Dec 12, 2016
+
+| Name | Version | Resource |
+|-----------|---------|----------|
+| cufflinks | 2.0.2 | Tusker |
+| cufflinks | 2.1.1 | Tusker |
+| cufflinks | 2.2 | Tusker |
+
+| | | |
+|-----------|-----|-------|
+| cufflinks | 2.1 | Crane |
+| cufflinks | 2.2 | Crane |
+
+
+
+Cufflinks
+(<a href="http://cufflinks.cbcb.umd.edu/" class="external-link">http://cufflinks.cbcb.umd.edu/</a>)
+is a transcript assembly program that includes a number of tools for
+analyzing RNA-Seq data. These tools assemble aligned RNA-Seq reads into
+transcripts, estimate their abundances, test for differential expression
+and regulation transcriptome-wide, and provide transcript
+quantification. Some of the tools part of Cufflinks can be run
+individually, while other are part of a larger workflow.
+
+The basic usage of Cufflinks is:
+
+**General Cufflinks Usage**
+
+``` syntaxhighlighter-pre
+cufflinks [options] input_alignments.[sam|bam]
+```
+
+where **input\_alignments.\[sam\|bam\]** is sorted input file of RNA-Seq
+read alignments in SAM/BAM format. The RNA-Seq read mapper
+TopHat/TopHat2 produces output in this format and is recommended to be
+used with Cufflinks, although SAM/BAM alignments produced from any
+aligner are accepted. More advanced Cufflinks options can be found in
+the
+manual: <a href="http://cufflinks.cbcb.umd.edu/manual.html" class="external-link">http://cufflinks.cbcb.umd.edu/manual.html</a>,
+or by typing:
+
+**Additional Cufflinks Options**
+
+``` syntaxhighlighter-pre
+[<username>@login.tusker ~]$ cufflinks -h
+```
+
+An example of how to run Cufflinks on Tusker with alignment file in SAM
+format, output directory *cufflinks\_output/* and 8 CPUs is shown below:
+
+**cufflinks.submit**
+
+\#!/bin/sh
+\#SBATCH --job-name=Cufflinks
+\#SBATCH --nodes=1
+\#SBATCH --ntasks-per-node=8
+\#SBATCH --time=168:00:00
+\#SBATCH --mem=50gb
+\#SBATCH --output=Cufflinks.%J.out
+\#SBATCH --error=Cufflinks.%J.err
+
+
+
+| |
+|---------------------------|
+| module load cufflinks/2.2 |
+
+cufflinks input\_alignments.sam -o cufflinks\_output/ -p
+$SLURM\_NTASKS\_PER\_NODE
+
+
+
+The program **cufflinks** produces number of files in its predefined
+output directory *cufflinks\_output/*. Some of the generated files are:
+
+- **transcripts.gtf**: The GTF file contains Cufflinks' assembled
+ isoforms where there is one GTF record per row, and each record
+ represents either a transcript or an exon within a transcript
+- **isoforms.fpkm\_tracking**: This file contains the estimated
+ isoform-level expression values in the generic FPKM Tracking Format
+- **genes.fpkm\_tracking**: This file contains the estimated
+ gene-level expression values in the generic FPKM Tracking Format
+
+
+
+Beside **cufflinks**, the Cufflinks package includes the following
+programs:
+
+- **Cuffcompare
+ **
+
+Cuffcompare uses the Cufflinks' GTF output as an input file and compares
+the assembled transcripts to a reference annotation. An example of
+comparing the already annotated genome **known\_annotation.gtf** with
+the new annotation **new\_annotation.gtf** follows:
+
+**General Cuffcompare Usage**
+
+``` syntaxhighlighter-pre
+cuffcompare -r known_annotation.gtf new_annotation.gtf
+```
+
+This tool reports various statistics about the transcripts, as well as a
+GTF file containing all transfrags in each sample.
+
+- **Cuffmerge**
+
+This program allows merging of multiple Cufflinks GTF files. An example
+of merging multiple GTF files with full paths defined in the file
+**list\_GTF.txt** and 8 CPUs is shown below:**
+**
+
+**General Cuffmerge Usage**
+
+``` syntaxhighlighter-pre
+cuffmerge list_GTF.txt -p 8
+```
+
+The cuffmerge output is single unified transcript file.
+
+- **Cuffdiff**
+
+Cuffdiff is used to identify differentially expressed transcripts. An
+example of **cuffdiff** for the annotated transcripts for the new
+genome, **new\_annotations.gtf,** with 3 SAM alignment files generated
+from TopHat and 8 CPUs follows:
+
+**General Cuffdiff Usage**
+
+``` syntaxhighlighter-pre
+cuffdiff new_alignments.gtf sample_1.sam, sample_2.sam, sample_3.sam -p 8
+```
+
+Cuffdiff prints multiple output files, such as: *FPKM tracking files*,
+*count tracking files*, *read group tracking files*, *differential
+expression tests*, *differential splicing tests*, *differential coding
+output*, *differential promoter use*, *read group info*, and *run info.*
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[cb\_cufflinks\_module.xsl](attachments/8193314/8127612.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_cufflinks\_version.xsl](attachments/8193314/8127613.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_cufflinks\_version.xsl](attachments/8193314/8127615.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193314/9863876.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193314/9863854.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193314/9863915.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193314/9863937.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193314/10387516.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193314/10387477.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193314/11632695.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193314/10944565.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193314/10944605.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193314/11632803.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193314/11632764.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193314/11632827.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193314/11632891.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193314/11632852.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193314/11632965.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193314/11632941.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193314/11633016.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193314/11633044.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193314/11633093.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193314/11633119.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193314/11633163.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193314/11633187.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193314/11633242.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193314/11633317.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193314/11633293.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193314/11633383.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193314/11633342.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193314/11633407.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193314/11633446.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193314/11633515.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193314/11633486.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193314/11633560.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193314/11633586.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193314/11633645.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193314/11633797.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193314/11633686.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193314/11633733.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193314/11633773.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193314/11633876.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193314/11633826.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193314/11634231.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193314/11633940.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193314/11633980.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193314/11634028.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193314/11634070.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193314/11634110.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8193314/11634159.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+
+Document generated by Confluence on Oct 24, 2018 14:54
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/bioinformatics_tools/removing_detecting_redundant_sequences/_index.md b/content/guides/running_applications/bioinformatics_tools/removing_detecting_redundant_sequences/_index.md
new file mode 100644
index 00000000..5cf83712
--- /dev/null
+++ b/content/guides/running_applications/bioinformatics_tools/removing_detecting_redundant_sequences/_index.md
@@ -0,0 +1,16 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Running Applications](Running-Applications_7471153.html)
+5. [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
+
+<span id="title-text"> HCC-DOCS : Tools for Removing/Detecting Redundant Sequences </span>
+==========================================================================================
+
+Created by <span class="author"> Adam Caprez</span> on Sep 04, 2014
+
+
+
+Document generated by Confluence on Oct 24, 2018 14:54
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/bioinformatics_tools/removing_detecting_redundant_sequences/cap3.md b/content/guides/running_applications/bioinformatics_tools/removing_detecting_redundant_sequences/cap3.md
new file mode 100644
index 00000000..3e154cf2
--- /dev/null
+++ b/content/guides/running_applications/bioinformatics_tools/removing_detecting_redundant_sequences/cap3.md
@@ -0,0 +1,160 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Running Applications](Running-Applications_7471153.html)
+5. [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
+6. [Tools for Removing/Detecting Redundant Sequences](8193310.html)
+
+<span id="title-text"> HCC-DOCS : CAP3 </span>
+==============================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified by
+<span class="editor"> Natasha Pavlovikj</span> on Dec 12, 2016
+
+| Name | Version | Resource |
+|------|---------|----------|
+| cap3 | 122107 | Crane |
+
+
+
+CAP3 (Contig Assembly Program) is a DNA sequence assembly program for
+small-scale assembly with or without quality values.
+
+The basic usage of CAP3 is:
+
+**General CAP3 Usage**
+
+``` syntaxhighlighter-pre
+cap3 input_reads.fasta [options] > output.txt
+```
+
+where **input\_reads.fasta** is an input file of sequence reads in fasta
+format, and **options** are optional parameters that can be found in the
+CAP3
+manual: <a href="http://computing.bio.cam.ac.uk/local/doc/cap3.txt" class="external-link">http://computing.bio.cam.ac.uk/local/doc/cap3.txt</a>.
+
+More information about the CAP3 program can be shown my typing:
+
+**Additional CAP3 Options**
+
+``` syntaxhighlighter-pre
+[<username>@login.crane ~]$ cap3
+```
+
+on the command line.
+
+An example of how to run basic CAP3 SLURM script on Crane is shown
+below:
+
+**cap3.submit**
+
+\#!/bin/sh
+\#SBATCH --job-name=CAP3
+\#SBATCH --nodes=1
+\#SBATCH --ntasks-per-node=1
+\#SBATCH --time=168:00:00
+\#SBATCH --mem=20gb
+\#SBATCH --output=CAP3.%J.out
+\#SBATCH --error=CAP3.%J.err
+
+
+
+| |
+|-------------------------|
+| module load cap3/122107 |
+
+cap3 input\_reads.fasta > output.txt
+
+CAP3 is single threaded program, and therefore both **\#SBATCH --nodes**
+and **\#SBATCH --ntasks-per-node** are set to **1**.
+
+
+
+**CAP3 Output**
+
+CAP3 returns few output files:
+*input\_reads.fasta.cap.singlets*, *input\_reads.fasta.cap.contigs**,*** *input\_reads.fasta.cap.contigs.links*, *input\_reads.fasta.cap.qual*, *input\_reads.fasta.cap.ace*, *input\_reads.fasta.cap.info*.
+
+The consensus fasta sequences are saved in the
+file ***input\_reads.fasta.cap.contigs***, while the reads that are not
+used in the assembly are stored in the fasta
+file ***input\_reads.fasta.cap.singlets***.
+
+
+
+**Useful Information**
+
+In order to test the CAP3 (cap3/122107) performance on Crane, we grouped
+separately three nucleotide datasets, **small.fasta**, **medium.fasta**
+and **large.fasta**. Some statistics about the input datasets and the
+time and memory resources required for CAP3 are shown on the table
+below:
+
+<table style="width:100%;">
+<colgroup>
+<col style="width: 14%" />
+<col style="width: 14%" />
+<col style="width: 14%" />
+<col style="width: 14%" />
+<col style="width: 14%" />
+<col style="width: 14%" />
+<col style="width: 14%" />
+</colgroup>
+<thead>
+<tr class="header">
+<th> </th>
+<th><p><strong>total # of sequences</strong></p></th>
+<th><p><strong>total # of bases</strong></p></th>
+<th><p><strong>total size in MB</strong></p></th>
+<th><p><strong>required time</strong></p></th>
+<th><p><strong>required memory</strong></p></th>
+<th># of used CPUs</th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td><p><strong>small.fasta</strong></p></td>
+<td><p>41,715</p></td>
+<td><p>35,581,740</p></td>
+<td><p>37.627 MB</p></td>
+<td><p>~ 1.6 hours</p></td>
+<td><p>~ 1.5 GB</p></td>
+<td>1</td>
+</tr>
+<tr class="even">
+<td><p><strong>medium.fasta</strong></p></td>
+<td><p>110,478</p></td>
+<td><p>147,543,113</p></td>
+<td><p>149 MB</p></td>
+<td><p>~ 2 hours</p></td>
+<td><p>~ 5 GB</p></td>
+<td>1</td>
+</tr>
+<tr class="odd">
+<td><p><strong>large.fasta</strong></p></td>
+<td><p>592,593</p></td>
+<td><p>827,629,204</p></td>
+<td><p>836 MB</p></td>
+<td><p>~ 12 hours</p></td>
+<td><p>~ 28 GB</p></td>
+<td>1</td>
+</tr>
+</tbody>
+</table>
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[cb\_cap3\_module.xsl](attachments/8193311/8127606.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_cap3\_version.xsl](attachments/8193311/8127607.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193311/8127608.xml)
+(application/octet-stream)
+
+Document generated by Confluence on Oct 24, 2018 14:54
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/bioinformatics_tools/removing_detecting_redundant_sequences/cd_hit.md b/content/guides/running_applications/bioinformatics_tools/removing_detecting_redundant_sequences/cd_hit.md
new file mode 100644
index 00000000..7c8cfd71
--- /dev/null
+++ b/content/guides/running_applications/bioinformatics_tools/removing_detecting_redundant_sequences/cd_hit.md
@@ -0,0 +1,118 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Running Applications](Running-Applications_7471153.html)
+5. [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
+6. [Tools for Removing/Detecting Redundant Sequences](8193310.html)
+
+<span id="title-text"> HCC-DOCS : CD-HIT </span>
+================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified by
+<span class="editor"> Natasha Pavlovikj</span> on Dec 12, 2016
+
+| Name | Version | Resource |
+|--------|---------|----------|
+| cd-hit | 4.6 | Crane |
+
+
+
+CD-HIT (Cluster Database at High Identity with Tolerance)
+(<a href="http://weizhong-lab.ucsd.edu/cd-hit/" class="external-link">http://weizhong-lab.ucsd.edu/cd-hit/</a>) is
+a program for clustering and comparing nucleotide or protein sequences.
+CD-HIT is very fast and can handle large DNA/RNA datasets.
+
+Some of the most frequently used executables from the CD-HIT package
+are: CD-HIT, CD-HIT-2D, CD-HIT-EST, CD-HIT-EST-2D, CD-HIT-454,
+CD-HIT-PARA, PSI-CD-HIT, CD-HIT-OTU, CD-HIT-LAP and CD-HIT-DUP:
+
+- <span style="line-height: 1.4285715;">CD-HIT or CD-HIT-EST clusters
+ similar proteins or DNAs into clusters that meet a defined
+ similarity threshold</span>
+- <span style="line-height: 1.4285715;">CD-HIT-2D (CD-HIT-EST-2D)
+ compares 2 datasets and identifies the sequences in db2 that are
+ similar to db1 above a given threshold</span>
+- <span style="line-height: 1.4285715;">CD-HIT-454 identifies natural
+ and artificial duplicates from pyrosequencing reads</span>
+- <span style="line-height: 1.4285715;">CD-HIT-OTU clusters rRNA tags
+ into OTUs</span>
+- <span style="line-height: 1.4285715;">CD-HIT-DUP identifies
+ duplicates from single or paired Illumina reads</span>
+- <span style="line-height: 1.4285715;">CD-HIT-LAP identifies
+ overlapping reads</span>
+
+<span style="line-height: 1.4285715;">Detailed overview of the whole
+CD-HIT package and executables can be found in the CD-HIT user's
+guide: <a href="http://weizhong-lab.ucsd.edu/cd-hit/wiki/doku.php?id=cd-hit_user_guide" class="external-link">http://weizhong-lab.ucsd.edu/cd-hit/wiki/doku.php?id=cd-hit_user_guide</a>.</span>
+
+The basic usage of CD-HIT is:
+
+**General CD-HIT Usage**
+
+``` syntaxhighlighter-pre
+cd-hit -i input_reads.fasta -o output [options]
+```
+
+where **input\_reads.fasta** is an input file of sequence reads in fasta
+format, **output** is the prefix of the output files,
+and **options** are optional parameters that can be found by typing:
+
+**Additional CD-HIT Options**
+
+``` syntaxhighlighter-pre
+[<username>@login.crane ~]$ cd-hit
+```
+
+<span style="line-height: 1.4285715;">CD-HIT is multi-threaded program,
+and therefore, using multiple threads is recommended. Thus, by setting
+the CD-HIT parameter **-T 0**, all CPUs defined in the SLURM script will
+be used. Setting the parameter **-M 0** allows unlimited usage of the
+available memory.</span>
+
+Simple SLURM CD-HIT script for Crane with 8 CPUs is given in addition:
+
+**cd-hit.submit**
+
+\#!/bin/sh
+\#SBATCH --job-name=CD-HIT
+\#SBATCH --nodes=1
+\#SBATCH --ntasks-per-node=8
+\#SBATCH --time=168:00:00
+\#SBATCH --mem=50gb
+\#SBATCH --output=CD-HIT.%J.out
+\#SBATCH --error=CD-HIT.%J.err
+
+
+
+| |
+|------------------------|
+| module load cd-hit/4.6 |
+
+cd-hit -i input\_reads.fasta -o output -M 0 -T 0
+
+
+
+**CD-HIT Output**
+
+CD-HIT prints 2 files: *output* and *output.clstr*.
+
+***Output*** contains the final clustered non-redundant sequences in
+fasta format, while ***output.clstr*** has an information about the
+clusters with associated sequences.
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[cb\_cdhit\_module.xsl](attachments/8193312/8127609.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_cdhit\_version.xsl](attachments/8193312/8127610.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/8193312/8127611.xml)
+(application/octet-stream)
+
+Document generated by Confluence on Oct 24, 2018 14:54
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/compiling_an_openmp_application.md b/content/guides/running_applications/compiling_an_openmp_application.md
new file mode 100644
index 00000000..87971852
--- /dev/null
+++ b/content/guides/running_applications/compiling_an_openmp_application.md
@@ -0,0 +1,56 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Running Applications](Running-Applications_7471153.html)
+5. [Compiling Source Code](Compiling-Source-Code_332258.html)
+
+<span id="title-text"> HCC-DOCS : Compiling an OpenMP Application </span>
+=========================================================================
+
+Created by <span class="author"> Derek Weitzel</span>, last modified on
+Nov 07, 2013
+
+Compiling an
+<a href="https://computing.llnl.gov/tutorials/openMP/" class="external-link">OpenMP</a>
+application is done with the `-fopenmp` option to gcc. For example, the
+command could be:
+
+``` syntaxhighlighter-pre
+$ gcc -o openmp-app.exe -fopenmp openmp-app.c
+```
+
+GCC will perform all of the OpenMP pragmas.
+
+OpenMP applications have OpenMP pragmas like `#pragma omp <options>`
+
+``` syntaxhighlighter-pre
+#pragma omp parallel for reduction(+: sum)
+ for (i = 0; i<NUM_STEPS; i++) {
+ x = 2.0 * (double)i / (double)(NUM_STEPS); /* value of x */
+ sum += x * x;
+ }
+```
+
+An example application code is
+[integrate\_mp.c](attachments/332316/5832705.c). Compiling
+integrate\_mp.c is done with the `gcc` command:
+
+``` syntaxhighlighter-pre
+$ gcc -o integrate_mp.exe -fopenmp integrate_mp.c
+```
+
+See [Submitting an OpenMP Job](Submitting-an-OpenMP-Job_332306.html) for
+instructions on how to submit `integrate_mp.exe` to the cluster.
+
+
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[integrate\_mp.c](attachments/332316/5832705.c)
+(application/octet-stream)
+
+Document generated by Confluence on Oct 24, 2018 14:48
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/compiling_source_code.md b/content/guides/running_applications/compiling_source_code.md
new file mode 100644
index 00000000..732a75ce
--- /dev/null
+++ b/content/guides/running_applications/compiling_source_code.md
@@ -0,0 +1,38 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Running Applications](Running-Applications_7471153.html)
+
+<span id="title-text"> HCC-DOCS : Compiling Source Code </span>
+===============================================================
+
+Created by <span class="author"> Derek Weitzel</span>, last modified by
+<span class="editor"> Adam Caprez</span> on Mar 19, 2018
+
+Compiling source code on HCC machines is done with compiler environments
+configured by the `module` utility. The utility adds directives to the
+environment and adds executables to the `PATH` so that users and jobs
+can directly call the compilers.
+
+Finding available compiler Modules
+----------------------------------
+
+``` syntaxhighlighter-pre
+$ module spider compiler
+```
+
+This command will list available compiler modules to load.
+
+Loading Modules
+---------------
+
+``` syntaxhighlighter-pre
+$ module load <module>
+```
+
+This command will load an available module. The modules are usually in
+the form of `<compiler>/<version>`.
+
+Document generated by Confluence on Oct 24, 2018 14:48
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/dmtcp_checkpointing.md b/content/guides/running_applications/dmtcp_checkpointing.md
new file mode 100644
index 00000000..56497312
--- /dev/null
+++ b/content/guides/running_applications/dmtcp_checkpointing.md
@@ -0,0 +1,1125 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Running Applications](Running-Applications_7471153.html)
+
+<span id="title-text"> HCC-DOCS : DMTCP (Checkpointing) </span>
+===============================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified by
+<span class="editor"> John Thiltges</span> on Sep 07, 2017
+
+| Name | Version | Resource |
+|-------|---------|----------|
+| dmtcp | 2.0 | Tusker |
+| dmtcp | 2.3 | Tusker |
+| dmtcp | 2.4 | Tusker |
+| dmtcp | 2.5 | Tusker |
+
+| | | |
+|-------|-----|-------|
+| dmtcp | 2.0 | Crane |
+| dmtcp | 2.3 | Crane |
+| dmtcp | 2.4 | Crane |
+| dmtcp | 2.5 | Crane |
+
+
+
+<a href="http://dmtcp.sourceforge.net/" class="external-link">DMTCP</a>
+(Distributed MultiThreaded Checkpointing) is a checkpointing package for
+applications. Using checkpointing allows resuming of a failing
+simulation due to failing resources (e.g. hardware, software, exceeded
+time and memory resources).
+
+DMTCP supports both sequential and multi-threaded applications. Some
+examples of binary programs on Linux distributions that can be used with
+DMTCP are OpenMP, MATLAB, Python, Perl, MySQL, bash, gdb, X-Windows etc.
+
+DMTCP provides support for several resource managers, including SLURM,
+the resource manager used in HCC. The DMTCP module is available both on
+Tusker and Crane, and is enabled by typing:
+
+| |
+|-----------------------|
+| module load dmtcp/2.5 |
+
+
+After the module is loaded, the first step is to run the command:
+
+
+
+**dmtcp\_launch**
+
+``` syntaxhighlighter-pre
+[<username>@login.tusker ~]$ dmtcp_launch --new-coordinator --rm --interval <interval_time_seconds> <your_command>
+```
+
+where **--rm** option enables SLURM support,
+**<interval\_time\_seconds>** is the time in seconds between
+automatic checkpoints, and **<your\_command>** is the actual
+command you want to run and checkpoint.
+
+Beside the general options shown above, more **dmtcp\_launch** options
+can be seen by using:
+
+**Additional dmtcp\_launch Options**
+
+``` syntaxhighlighter-pre
+[<username>@login.tusker ~]$ dmtcp_launch --help
+```
+
+**dmtcp\_launch** creates few files that are used to resume the
+cancelled job, such as *ckpt\_\*.dmtcp* and
+*dmtcp\_restart\_script\*.sh*. Unless otherwise stated
+(using **--ckptdir** option), these files are stored in the current
+working directory.
+
+
+The second step of DMTCP is to restart the cancelled job, and there are
+two ways of doing that:
+
+- **dmtcp\_restart ckpt\_\*.dmtcp** *<options>* (before running
+ this command delete any old *ckp\_\*.dmtcp* files in your current
+ directory)
+
+<!-- -->
+
+- **./dmtcp\_restart\_script.sh** *<options>*
+
+If there are no options defined in the *<options>* field, DMTCP
+will keep running with the options defined in the initial
+**dmtcp\_launch** call (such as interval time, output directory etc).
+
+
+Simple example of using DMTCP with
+[BLAST](Running-BLAST-Alignment_8193291.html) on Tusker is shown below:
+
+**dmtcp\_blastx.submit**
+
+\#!/bin/sh
+\#SBATCH --job-name=BlastX
+\#SBATCH --nodes=1
+\#SBATCH --ntasks=8
+\#SBATCH --time=50:00:00
+\#SBATCH --mem=20gb
+\#SBATCH --output=BlastX\_info\_1.txt
+\#SBATCH --error=BlastX\_error\_1.txt
+
+
+| |
+|-----------------------|
+| module load dmtcp/2.5 |
+
+| |
+|-----------------------|
+| module load blast/2.4 |
+
+cd $WORK/<project\_folder>
+cp -r /work/HCC/DATA/blastdb/nr/ /tmp/
+cp <span style="line-height: 1.4285715;">input\_reads.fasta</span> /tmp/
+
+dmtcp\_launch --new-coordinator --rm --interval 3600 blastx -query
+/tmp/input\_reads.fasta -db /tmp/nr/nr -out blastx\_output.alignments
+-num\_threads $SLURM\_NTASKS\_PER\_NODE
+
+In this example, DMTCP takes checkpoints every hour (**--interval
+3600**), and the actual command we want to checkpoint is **blastx** with
+some general BLAST options defined with *-query*, *-db*, *-out*,
+*-num\_threads*.
+
+If this job is killed for various reasons, it can be restarted using the
+following submit file:
+
+**dmtcp\_restart\_blastx.submit**
+
+\#!/bin/sh
+\#SBATCH --job-name=BlastX
+\#SBATCH --nodes=1
+\#SBATCH --ntasks=8
+\#SBATCH --time=50:00:00
+\#SBATCH --mem=20gb
+\#SBATCH --output=BlastX\_info\_2.txt
+\#SBATCH --error=BlastX\_error\_2.txt
+
+
+| |
+|-----------------------|
+| module load dmtcp/2.5 |
+
+| |
+|-----------------------|
+| module load blast/2.4 |
+
+cd $WORK/<project\_folder>
+cp -r /work/HCC/DATA/blastdb/nr/ /tmp/
+<span style="line-height: 1.4285715;">cp </span><span
+style="line-height: 1.4285715;">input\_reads.fasta</span><span
+style="line-height: 1.4285715;"> /tmp/</span>
+
+\# Start DMTCP \#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#
+dmtcp\_coordinator --daemon --port 0 --port-file /tmp/port
+export DMTCP\_COORD\_HOST=\`hostname\`
+export DMTCP\_COORD\_PORT=$(</tmp/port)
+
+\# Restart job \#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#
+./dmtcp\_restart\_script.sh
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-warning confluence-information-macro-icon"></span>
+
+**dmtcp\_restart** generates new
+*ckpt\_\*.dmtcp* and *dmtcp\_restart\_script\*.sh* files. Therefore, if
+the restarted job is also killed due to unavailable/exceeded resources,
+you can resubmit the same job again without any changes in the submit
+file shown above (just don't forget to delete the old *ckpt\_\*.dmtcp*
+files if you are using these files instead of
+*dmtcp\_restart\_script.sh*)
+
+
+Even though DMTCP tries to support most mainstream and commonly used
+applications, there is no guarantee that every application can be
+checkpointed and restarted.
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[cb\_blast\_module.xsl](attachments/10813466/10944522.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_dmtcp\_version.xsl](attachments/10813466/10944523.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/10944524.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/10944525.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_dmtcp\_version.xsl](attachments/10813466/10944526.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[cb\_dmtcp\_module.xsl](attachments/10813466/10944527.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/17042009.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/17042044.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/17042094.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/17042129.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/17042214.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/17042249.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/17042299.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/17042334.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/17042392.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/17042427.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/17042481.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/17042552.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/17042517.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/17042604.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/17042639.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/17042713.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/17042748.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/17042799.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/17042834.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/17042940.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/17042890.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/17043009.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/17042974.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/17043069.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/17043104.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/17043205.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/17043155.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/17043240.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/17043295.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/17043330.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/17043382.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/17043417.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/17043478.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/17043549.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/17043514.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/17043600.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/17043635.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/17043721.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/17043756.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/17043806.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/17043841.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/17043900.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/17043935.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/17043990.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/17044025.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/17044075.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/17044144.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/17044109.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/17044196.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/17044231.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/17044283.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/17044318.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/17044377.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/17044416.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/17044481.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/17044520.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/17044577.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/17044616.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/17044674.xml) (text/xml)
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+[crane\_modules.xml](attachments/10813466/30444794.xml) (text/xml)
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/30444896.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/30444934.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/30445066.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+[crane\_modules.xml](attachments/10813466/30445168.xml) (text/xml)
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+[tusker\_modules.xml](attachments/10813466/30445206.xml) (text/xml)
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+[crane\_modules.xml](attachments/10813466/30445270.xml) (text/xml)
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+[tusker\_modules.xml](attachments/10813466/30445536.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/30445610.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/30445648.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/30445713.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/30445751.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/30445816.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/30445925.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/30446140.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/30446246.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/30446284.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+[crane\_modules.xml](attachments/10813466/30446883.xml) (text/xml)
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+[tusker\_modules.xml](attachments/10813466/30446921.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/30447045.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/30447216.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/30447254.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/30447316.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/30447478.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/30447357.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/30447398.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/30447439.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/30447544.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/30447582.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/30447717.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/30447655.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/30447755.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/30447817.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/30447990.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/30447894.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/30447952.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/30448052.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/30448090.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/30448401.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/30448531.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/30448666.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/30448577.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/30448628.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/30448731.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/30448769.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/30448838.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/30448876.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/30448946.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/30448984.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/33685571.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/33685605.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/33685682.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/33685716.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/33685794.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/33685828.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/33685899.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/33685933.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/33686036.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/33686070.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/33686140.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/33686174.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/33686279.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/33686313.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/33687815.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/33687849.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/33688421.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/33688457.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/33689748.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/33689782.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/33689968.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/33690002.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/35323977.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/35324042.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/35324087.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/35324152.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/35324425.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/35324622.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/35324555.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/35324845.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/35324912.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/35325010.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/35325644.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/35325179.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/35325222.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/35325265.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/35325572.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/35325689.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/35325757.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/35326150.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/35326744.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/35326676.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[crane\_modules.xml](attachments/10813466/17042004.xml) (text/xml)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/10813466/17042005.xml) (text/xml)
+
+Document generated by Confluence on Oct 24, 2018 14:54
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/installing_perl_modules.md b/content/guides/running_applications/installing_perl_modules.md
new file mode 100644
index 00000000..f0742761
--- /dev/null
+++ b/content/guides/running_applications/installing_perl_modules.md
@@ -0,0 +1,68 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Running Applications](Running-Applications_7471153.html)
+
+<span id="title-text"> HCC-DOCS : Installing Perl modules </span>
+=================================================================
+
+Created by <span class="author"> John Thiltges</span>, last modified by
+<span class="editor"> Adam Caprez</span> on Dec 09, 2016
+
+If you need additional Perl modules, they can be installed into your
+home directory. We recommend using
+<a href="https://store.continuum.io/cshop/anaconda/" class="external-link">Anaconda</a> to
+create an environment with a self-contained, independent Perl install.
+ This will eliminate any conflicts from the system Perl version and
+allow modules to be installed via `cpan` or `cpanminus`.
+
+Create an environment with Perl installed
+-----------------------------------------
+
+The following commands will create an environment called `myperl`, with
+Perl and cpanminus installed.
+
+**Create myperl environment**
+
+``` syntaxhighlighter-pre
+module load anaconda
+conda create -n myperl perl perl-app-cpanminus
+```
+
+Activate the environment
+------------------------
+
+To use the environment, it must be *activated.*
+
+Job submission
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-warning confluence-information-macro-icon"></span>
+
+To use your created environment and installed modules in a SLURM job,
+the following lines must be included ahead of running any Perl program.
+
+**Activate environment**
+
+``` syntaxhighlighter-pre
+module load anaconda
+source activate myperl
+```
+
+
+
+<span style="color: rgb(0,0,0);font-size: 20.0px;">Installing a module
+from CPAN</span>
+
+Once the environment is activated, modules can be installed via
+`cpan `or `cpanm `with no special configuration needed.
+
+**Install a module**
+
+``` syntaxhighlighter-pre
+cpanm My::Module
+```
+
+Document generated by Confluence on Oct 24, 2018 14:54
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/module_commands.md b/content/guides/running_applications/module_commands.md
new file mode 100644
index 00000000..55216587
--- /dev/null
+++ b/content/guides/running_applications/module_commands.md
@@ -0,0 +1,175 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Running Applications](Running-Applications_7471153.html)
+
+<span id="title-text"> HCC-DOCS : Module Commands </span>
+=========================================================
+
+Created by <span class="author"> William Hurst</span>, last modified by
+<span class="editor"> Derek Weitzel</span> on Aug 19, 2013
+
+<span id="4"></span>
+
+`module` commands provide an HPC system user the capability to compile
+into their **source code** using any **type of library** that is
+available on the server. The `module` command gives each user the
+ability to modify their environmental PATH and LD\_LIBRARY\_PATH
+variables.
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-warning confluence-information-macro-icon"></span>
+
+Please note that if you compile your application using a particular
+module, you must include the appropriate module load statement in your
+submit script.
+
+List Modules Loaded
+-------------------
+
+**Example Usage: module list**
+
+``` syntaxhighlighter-pre
+module list
+
+No Modulefiles Currently Loaded.
+
+echo $PATH
+/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin
+```
+
+List Modules Available
+----------------------
+
+**Listing Modules Available**
+
+``` syntaxhighlighter-pre
+module avail
+
+---------------------------------------------- /util/opt/Modules/modulefiles ----------------------------------------------
+NCL/6.0 bowtie/2.0.0-beta6 compiler/pgi/12 hdfeos5/1.14 mplus/7.0 szip/2.1
+NCL/6.0dist compiler/gcc/4.6 cufflinks/2.0.2 hugeseq/1.0 netcdf/4.1 tophat/2.0.5
+NCO/4.1 compiler/gcc/4.7 deprecated intel-mkl/11 netcdf/4.2 udunits/2.1
+R/2.15 compiler/intel/11 hdf4/4.2 intel-mkl/12 openmpi/1.5 zlib/1.2
+WRF/WRF compiler/intel/12 hdf5/1.8 lsdyna/5.1.1 openmpi/1.6
+acml/5.1 compiler/open64/4.5 hdf5/1.8.6 lsdyna/6.0.0 samtools/0.1
+bowtie/0.12.8 compiler/pgi/11 hdfeos2/2.18 mplus/6.12 sas/9.3
+```
+
+module load <a href="/pages/createpage.action?spaceKey=HCCDOC&title=module-name&linkCreation=true&fromPageId=332464" class="createlink">module-name</a>
+-------------------------------------------------------------------------------------------------------------------------------------------------------------------
+
+**Places** the binaries and libraries for
+<a href="/pages/createpage.action?spaceKey=HCCDOC&title=module-name&linkCreation=true&fromPageId=332464" class="createlink">module-name</a>
+into your PATH and LD\_LIBRARY\_PATH
+
+**Example Usage: Loading Desired Module**
+
+``` syntaxhighlighter-pre
+
+module load compiler/pgi/11
+
+module list
+Currently Loaded Modulefiles:
+ 1) compiler/pgi/11
+
+echo $PATH
+/util/comp/pgi/linux86-64/11/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin
+
+```
+
+module unload <a href="/pages/createpage.action?spaceKey=HCCDOC&title=module-name&linkCreation=true&fromPageId=332464" class="createlink">module-name</a>
+---------------------------------------------------------------------------------------------------------------------------------------------------------------------
+
+**Removes** the binaries and libraries associated with
+<a href="/pages/createpage.action?spaceKey=HCCDOC&title=module-name&linkCreation=true&fromPageId=332464" class="createlink">module-name</a>
+from your PATH and LD\_LIBRAY\_PATH
+
+**Example Usage: module unload**
+
+``` syntaxhighlighter-pre
+module unload compiler/pgi/11
+
+module list
+No Modulefiles Currently Loaded.
+
+echo $PATH
+/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin
+
+```
+
+module purge
+------------
+
+**Purges** all previously **loaded** module libraries and binaries from
+your PATH and LD\_LIBRARY\_PATH
+
+**Example Usage: module purge**
+
+``` syntaxhighlighter-pre
+module load compiler/open64
+module load zlib/1.2
+
+
+module list
+
+
+Currently Loaded Modulefiles:
+ 1) zlib/1.2 2) compiler/open64/4.5
+
+
+module purge
+
+
+module list
+
+No Modulefiles Currently Loaded.
+```
+
+module help
+-----------
+
+To see a complete list of module commands/options.
+
+**Example Usage: module help**
+
+``` syntaxhighlighter-pre
+module help
+Modules Release Tcl 1.144 Copyright GNU GPL v2 1991
+Usage: module [ command ]
+Commands:
+ list [switches] modulefile [modulefile ...]
+ display | show modulefile [modulefile ...]
+ add | load modulefile [modulefile ...]
+ purge | rm | unload modulefile [modulefile ...]
+ reload modulefile [modulefile ...]
+ switch | swap [oldmodulefile] newmodulefile
+ avail [switches] [modulefile [modulefile ...]]
+ aliases
+ whatis [modulefile [modulefile ...]]
+ help [modulefile [modulefile ...]]
+ path modulefile
+ paths modulefile
+ initlist modulefile
+ initadd modulefile
+ initrm modulefile
+ initclear modulefile
+ initprepend modulefile
+ use dir [dir ...]
+ unuse dir [dir ...]
+ source scriptfile
+ apropos | keyword | search string
+Switches:
+ -t terse format avail and list
+ -l long format avail and list
+```
+
+
+
+
+
+
+
+Document generated by Confluence on Oct 24, 2018 14:48
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/running_gaussian_at_hcc.md b/content/guides/running_applications/running_gaussian_at_hcc.md
new file mode 100644
index 00000000..02221d09
--- /dev/null
+++ b/content/guides/running_applications/running_gaussian_at_hcc.md
@@ -0,0 +1,274 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Running Applications](Running-Applications_7471153.html)
+
+<span id="title-text"> HCC-DOCS : Running Gaussian at HCC </span>
+=================================================================
+
+Created by <span class="author"> Jun Wang</span>, last modified by <span
+class="editor"> Carrie Brown</span> on Dec 14, 2017
+
+Gaussian is a popular ab inito quantum chemistry program in the field of
+computational chemistry. Gaussian is a licensed program and currently
+University of Nebraska-Lincoln (UNL) owns a campus wide site license for
+its source codes \[G09 Src Minor Rev. (D.01)\] and a couple of
+pre-compiled binaries.
+
+All faculty/staff/students of UNL are allowed to access **g09** source
+code and run the **g09** program at HCC. Collaborators of UNL faculty
+may be allowed to run **g09** binaries while they are physically
+visiting UNL. Note that faculty/staff/students from other branches of
+University of Nebraska (NU) system including University of Nebraska
+Omaha, University of Nebraska Medical Center, University of Nebraska at
+Kearney are not allowed to run **g09** program at HCC without purchase
+of a **g09** license.
+
+For access, contact us
+at <a href="mailto:hcc-support@unl.edu?subject=Request+access+to+Gaussian+group" class="external-link">hcc-support@unl.edu</a> and
+include your HCC username. After your account has been added to the
+group "*gauss*", here are four simple steps to run Gaussian 09 on
+Sandhills, Tusker, and Crane:
+
+**Step 1:** Copy **g09** sample input file and SLURM script to your
+"g09" test directory on the */work* filesystem:
+
+**Copy sample files**
+
+``` syntaxhighlighter-pre
+cd $WORK
+mkdir g09-test
+cd g09-test
+cp /util/opt/gaussian/09/RevD/test_g98.com ./
+cp /util/opt/gaussian/09/RevD/run-g09-general.slurm ./
+```
+
+**Step 2:** Check **g09** input file and modify it if necessary:
+
+**Review g09 input file**
+
+``` syntaxhighlighter-pre
+vi test_g98.com
+```
+
+<span style="color: rgb(0,0,0);">Content of Gaussian input file
+"*test\_g98.com*":</span>
+
+**Input file test\_g98.com**
+
+%nprocs=4
+\#P RHF/6-31G\*\* scf=direct test prop=fit
+
+Gaussian Test Job 178:
+TATB rhf/6-31g\*\*//hf/6-31g\*\*
+Energy with tight cutoffs would be -1006.2213391, is -1006.2213170
+with
+default cutoffs
+
+0,1
+X
+C,1,RC1
+C,1,RC2,2,60.
+C,1,RC1,3,60.,2,180.,0
+C,1,RC2,4,60.,3,180.,0
+C,1,RC1,5,60.,4,180.,0
+C,1,RC2,6,60.,5,180.,0
+
+... ...
+
+N,7,RCN2,13,90.,1,180.,0
+H,29,RNH,7,A2,13,0.,0
+H,29,RNH,7,A2,13,180.,0
+
+RC1=1.431682
+RC2=1.451892
+RCN1=1.431748
+RNO=1.205098
+A1=120.501393
+RCN2=1.312086
+RNH=0.990828
+A2=118.920716
+
+**Step 3:** Check **g09** SLURM submission script file, and modify it if
+necessary:
+
+**Review SLURM submission script**
+
+``` syntaxhighlighter-pre
+vi run-g09-general.slurm
+```
+
+<span style="line-height: 1.42857;">Content of Gaussian SLURM submission
+file</span><span
+style="color: rgb(0,0,0);"> "*run-g09-general.slurm*"</span><span
+style="line-height: 1.42857;">:</span>
+
+**run-g09-general.slurm**
+
+``` syntaxhighlighter-pre
+#!/bin/sh
+#SBATCH -J g09
+#SBATCH --nodes=1 --ntasks-per-node=4
+#SBATCH --mem-per-cpu=2000
+#SBATCH --time=01:00:00
+#SBATCH --partition=batch
+#SBATCH --error=TestJob.%J.stderr
+#SBATCH --output=TestJob.%J.stdout
+
+nodelist > ./machines.LINUX
+echo $SLURM_JOB_ID > ./jobid
+
+module load gaussian/09/RevD
+source ${g09root}/g09/bsd/g09.profile
+export GAUSS_SCRDIR=$TMPDIR
+
+g09 test_g98.com
+```
+
+<span style="line-height: 1.42857;">**Step 4:** Submit the job and wait
+for **g09** job to be started by the scheduler:</span>
+
+**Submit job**
+
+``` syntaxhighlighter-pre
+sbatch run-g09-general.slurm
+```
+
+Note that your account has to be a member of group "**gauss**" to run
+such example.
+
+
+
+**Some g09 restrictions you need to know:**
+
+1. Parallel execution of our g09 is Open-MP based:
+ This means you can run **g09** only on a single node with multiple
+ CPUs, e.g.
+ **\#SBATCH --nodes=1 --ntasks-per-node=4** with SLURM.
+ Also, make sure “**%nprocs=4**” in g09 input file matches with your
+ CPU request in your SLURM submission file.
+2. Scratch files directory for g09:
+ On Tusker: **GAUSS\_SCRDIR=$TMPDIR**
+ On Sandhills: **GAUSS\_SCRDIR=$TMPDIR**
+ You may override the default scratch file location by explicitly
+ specifying it in your SLURM submission file for Gaussian (ie.
+ **export GAUSS\_SCRDIR=$PWD**).
+3. Convert .chk file to .fchk file before loading to GaussianView:
+ Type “**module load gaussian/09/RevD;source
+ ${g09root}/g09/bsd/g09.profile**" to load g09 environment.
+ Type "**cd xxx**" to change directory, where xxx is the directory
+ including the g09 generated .chk file.
+ Type "**formchk yyy.chk yyy.fchk**" to convert format, where yyy is
+ the file name of your .chk file before the suffix.
+
+
+
+**Run g09 with [DMTCP (Checkpointing)](10813466.html):**
+
+If your **g09** job could not finish within 168 hours walltime, you may
+try the following steps to checkpoint your **g09** job with dmtcp and
+resume the interrupted job afterwards.
+
+<span style="color: rgb(0,0,0);">1. Submit your initial **g09** job with
+the following SLURM submission file:</span>
+
+**Submit with dmtcp**
+
+``` syntaxhighlighter-pre
+#!/bin/sh
+#SBATCH -J g09-dmtcp
+#SBATCH --nodes=1 --ntasks-per-node=16
+#SBATCH --mem-per-cpu=4000
+#SBATCH --time=168:00:00
+#SBATCH --partition=batch
+#SBATCH --error=TestJob.%J.stderr
+#SBATCH --output=TestJob.%J.stdout
+
+nodelist > ./machines.LINUX
+echo $SLURM_JOB_ID > ./jobid
+
+module load gaussian/09/RevD
+source ${g09root}/g09/bsd/g09.profile
+export GAUSS_SCRDIR=$PWD
+
+rm -rf ckpt*
+rm -rf dmtcp*
+
+module load dmtcp/2.4
+
+export DMTCP_CHECKPOINT_INTERVAL=561600
+export DMTCP_HOST=localhost
+export DMTCP_PORT=7779
+export DMTCP_GZIP=1
+export DMTCP_CHECKPOINT_DIR=$PWD
+export DMTCP_SIGCKPT=12
+export DMTCP_TMPDIR=/tmp
+
+dmtcp_checkpoint g09 < au3O2-c13-pbepbegd3iop30-opt-tz.gjf > au3O2-c13-pbepbegd3iop30-opt-tz.log
+```
+
+<span style="color: rgb(0,0,0);">One parameter you may need to adjust
+is** **</span><span
+style="color: rgb(0,0,0);">**DMTCP\_CHECKPOINT\_INTERVAL** which
+controls the time interval in seconds for writing dmtcp checkpoint
+files. Currently it is set to 561600s, namely 156 hours. In other words,
+dmtcp will begin to write checkpointing files 12 hrs before the total
+168 hrs walltime. The time to finish writing checkpointing files will
+vary with different types of **g09** calculations. I would suggest you
+to try different </span><span
+style="color: rgb(0,0,0);">**DMTCP\_CHECKPOINT\_INTERVAL** values in
+your submitted g09-dmtcp jobs to find a suitable value for your
+particular type of calculation.</span>
+
+<span style="color: rgb(0,0,0);"><span style="color: rgb(0,0,0);"><span
+style="color: rgb(0,0,0);">2. Once your running job completed
+checkpointing, make sure you see a file
+called **dmtcp\_restart\_script.sh** generated in your job's working
+directory. Then you can use the following SLURM submission file to
+resume your interrupted job:</span></span></span>
+
+**Resume with dmtcp**
+
+``` syntaxhighlighter-pre
+#!/bin/sh
+#SBATCH -J g09-restart
+#SBATCH --nodes=1 --ntasks-per-node=16
+#SBATCH --mem-per-cpu=4000
+#SBATCH --time=168:00:00
+#SBATCH --partition=batch
+#SBATCH --error=TestJob.%J.stderr
+#SBATCH --output=TestJob.%J.stdout
+
+nodelist > ./machines.LINUX
+echo $SLURM_JOB_ID > ./jobid
+
+module load gaussian/09/RevD
+source ${g09root}/g09/bsd/g09.profile
+export GAUSS_SCRDIR=$PWD
+
+module load dmtcp/2.4
+
+export DMTCP_CHECKPOINT_INTERVAL=561600
+export DMTCP_HOST=localhost
+export DMTCP_PORT=7779
+export DMTCP_GZIP=1
+export DMTCP_CHECKPOINT_DIR=$PWD
+export DMTCP_SIGCKPT=12
+export DMTCP_TMPDIR=/tmp
+
+./dmtcp_restart_script.sh
+```
+
+Note
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-warning confluence-information-macro-icon"></span>
+
+<span style="color: rgb(0,0,0);">The restarted job **will not** write
+the new output to the original output file
+"*au3O2-c13-pbepbegd3iop30-opt-tz.log*", but to the
+file "**TestJob.%J.stdout**" instead.</span>
+
+Document generated by Confluence on Oct 24, 2018 14:54
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/running_ocean_land_atmosphere_model_olam.md b/content/guides/running_applications/running_ocean_land_atmosphere_model_olam.md
new file mode 100644
index 00000000..f989da63
--- /dev/null
+++ b/content/guides/running_applications/running_ocean_land_atmosphere_model_olam.md
@@ -0,0 +1,1536 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Running Applications](Running-Applications_7471153.html)
+
+<span id="title-text"> HCC-DOCS : Running Ocean Land Atmosphere Model (OLAM) </span>
+====================================================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified by
+<span class="editor"> Jingchao Zhang</span> on Aug 12, 2016
+
+<span class="underline">OLAM compilation on Tusker</span>
+=========================================================
+
+<span style="color: rgb(255,0,0);"><span
+style="color: rgb(51,102,255);">**pgi/11 compilation with mpi and openmp
+enabled**</span>
+</span>
+
+1. Load modules. Command: "**module load compiler/pgi/11 openmpi/1.6
+ szip/2.1 zlib/1.2 NCL/6.1dist**"
+2. Edit the include.mk file.
+
+``` syntaxhighlighter-pre
+#----------------- LINUX Intel Fortran ifort/gcc ---------------
+F_COMP=mpif90
+# If the compiler supports (and the user wants to use)
+# the module IEEE_ARITHMETIC, uncomment below
+IEEE_ARITHMETIC=yes
+# If using MPI libraries:
+OLAM_MPI=yes
+# If parallel hdf5 is supported, uncomment the next line
+OLAM_PARALLEL_HDF5=yes
+# If you use the ED2 model, uncomment the next line
+#USE_ED2=yes
+MPI_PATH=/util/opt/openmpi/1.6/pgi/11
+PAR_INCS=-I$(MPI_PATH)/include:$(MPI_PATH)/lib
+PAR_LIBS=-L$(MPI_PATH)/lib -lmpi
+# OPTIMIZED:
+F_OPTS=-O3 -traceback -mp
+#F_OPTS=-xHost -O3 -fno-alias -ip -openmp -traceback
+#F_OPTS=-g -O3 -xHost -traceback
+# DEBUG:
+#F_OPTS=-g -fp-model precise -check bounds -traceback \
+# -debug extended -check uninit -ftrapuv
+# FORTRAN FLAGS FOR BIG FILES WHICH WOULD HAVE EXCESSIVE COMPILATION TIME
+#SLOW_FFLAGS=-O1 -g -no-ip -traceback
+C_COMP=mpicc
+#C_COMP=mpicc
+C_OPTS=-DUNDERSCORE -DLITTLE
+NCARG_DIR=/util/src/ncl_ncarg/ncl_ncarg-6.1.2/lib
+LIBNCARG=-L$(NCARG_DIR) -lncarg -lncarg_gks -lncarg_c \
+ -L/usr/lib64 -lX11 -ldl -lpthread -lgfortran -lcairo
+HDF5_LIBS=-L/util/opt/hdf5/1.8.13/openmpi/1.6/pgi/11/lib -lhdf5_fortran -lhdf5 -lz -lm
+HDF5_INCS=-I/util/opt/hdf5/1.8.13/openmpi/1.6/pgi/11/include
+NETCDF_LIBS=-L/util/opt/netcdf/4.2/pgi/11/lib -lnetcdf
+NETCDF_INCS=-I/util/opt/netcdf/4.2/pgi/11/include
+
+LOADER=$(F_COMP)
+LOADER_OPTS=-mp
+#LOADER_OPTS=-static-intel $(F_OPTS)
+# For Apple OSX: the stack size needs to be increased at link time
+# LOADER_OPTS=-static-intel $(F_OPTS) -Wl,-stack_size -Wl,0x10000000
+# to allow ifort compiler to link with pg-compiled ncar graphics:
+# LIBS=-z muldefs -L/opt/pgi/linux86-64/5.2/lib -lpgftnrtl -lpgc
+## IMPORTANT: Need to specify this flag in ED2
+#USE_HDF5=1
+```
+
+ 3. Command: "**make clean**"
+
+ 4. Command: "**make -j 8**"
+
+
+
+<span style="color: rgb(51,102,255);">**intel/12 compilation with mpi
+and openmp enabled**</span>
+
+1. Load modules. Command: "**module load compiler/intel/12 openmpi/1.6
+ szip/2.1 zlib/1.2**"
+2. Edit the include.mk file.
+
+``` syntaxhighlighter-pre
+ #----------------- LINUX Intel Fortran ifort/gcc ---------------
+F_COMP=mpif90
+# If the compiler supports (and the user wants to use)
+# the module IEEE_ARITHMETIC, uncomment below
+IEEE_ARITHMETIC=yes
+# If using MPI libraries:
+OLAM_MPI=yes
+# If parallel hdf5 is supported, uncomment the next line
+OLAM_PARALLEL_HDF5=yes
+# If you use the ED2 model, uncomment the next line
+#USE_ED2=yes
+MPI_PATH=/util/opt/openmpi/1.6/intel/12
+PAR_INCS=-I$(MPI_PATH)/include:$(MPI_PATH)/lib
+PAR_LIBS=-L$(MPI_PATH)/lib -lmpi
+# OPTIMIZED:
+F_OPTS=-O3 -traceback -openmp
+#F_OPTS=-xHost -O3 -fno-alias -ip -openmp -traceback
+#F_OPTS=-g -O3 -xHost -traceback
+# DEBUG:
+#F_OPTS=-g -fp-model precise -check bounds -traceback \
+# -debug extended -check uninit -ftrapuv
+# FORTRAN FLAGS FOR BIG FILES WHICH WOULD HAVE EXCESSIVE COMPILATION TIME
+#SLOW_FFLAGS=-O1 -g -no-ip -traceback
+C_COMP=mpicc
+#C_COMP=mpicc
+C_OPTS=-DUNDERSCORE -DLITTLE
+NCARG_DIR=/util/src/ncl_ncarg/ncl_ncarg-6.1.2/lib
+LIBNCARG=-L$(NCARG_DIR) -lncarg -lncarg_gks -lncarg_c \
+ -L/usr/lib64 -lX11 -ldl -lpthread -lgfortran -lcairo
+HDF5_LIBS=-L/util/opt/hdf5/1.8.13/openmpi/1.6/intel/12/lib -lhdf5_fortran -lhdf5 -lz -lm
+HDF5_INCS=-I/util/opt/hdf5/1.8.13/openmpi/1.6/intel/12/include
+NETCDF_LIBS=-L/util/opt/netcdf/4.2/intel/12/lib -lnetcdf
+NETCDF_INCS=-I/util/opt/netcdf/4.2/intel/12/include
+LOADER=$(F_COMP)
+LOADER_OPTS=-openmp
+#LOADER_OPTS=-static-intel $(F_OPTS)
+# For Apple OSX: the stack size needs to be increased at link time
+# LOADER_OPTS=-static-intel $(F_OPTS) -Wl,-stack_size -Wl,0x10000000
+# to allow ifort compiler to link with pg-compiled ncar graphics:
+# LIBS=-z muldefs -L/opt/pgi/linux86-64/5.2/lib -lpgftnrtl -lpgc
+## IMPORTANT: Need to specify this flag in ED2
+#USE_HDF5=1
+```
+
+ 3. Command: "**make clean**"
+
+ 4. Command: "**make -j 8**"
+
+
+
+<span class="underline">OLAM compilation on Crane</span>
+========================================================
+
+<span style="color: rgb(51,102,255);">**Intel/15 compiler with
+OpenMPI/1.10**</span>
+
+1. Load modules. Command: "**<span style="color: rgb(0,0,0);">module
+ load compiler/intel/15 openmpi/1.10 NCL/6.1 netcdf/4.4 phdf5/1.8 szip/2.1 zlib/1.2</span>**<span
+ style="color: rgb(33,33,33);line-height: 1.4285715;">"</span>
+2. Edit the include.mk file:
+
+ ``` syntaxhighlighter-pre
+ #----------------- LINUX Intel Fortran ifort/gcc ---------------
+ F_COMP=/util/opt/hdf5/1.8/openmpi/1.10/intel/15/bin/h5pfc
+
+ # If the compiler supports (and the user wants to use)
+ # the module IEEE_ARITHMETIC, uncomment below
+ IEEE_ARITHMETIC=yes
+
+ # If using MPI libraries:
+ OLAM_MPI=yes
+
+ # If parallel hdf5 is supported, uncomment the next line
+ OLAM_PARALLEL_HDF5=yes
+
+ # If you use the ED2 model, uncomment the next line
+ #USE_ED2=yes
+
+ #MPI_PATH=/usr/local/mpich
+ PAR_INCS=-I/util/opt/openmpi/1.10/intel/15/include
+ PAR_LIBS=-L/util/opt/openmpi/1.10/intel/15/lib
+
+ # OPTIMIZED:
+ F_OPTS=-xHost -O3 -fno-alias -ip -openmp -traceback
+ #F_OPTS=-g -O3 -xHost -traceback
+
+ # DEBUG:
+ #F_OPTS=-g -fp-model precise -check bounds -traceback \
+ # -debug extended -check uninit -ftrapuv
+
+ # EXTRA OPTIONS FOR FIXED-SOURCE CODE
+ FIXED_SRC_FLAGS=-fixed -132
+
+ # FORTRAN FLAGS FOR BIG FILES WHICH WOULD HAVE EXCESSIVE COMPILATION TIME
+ SLOW_FFLAGS=-O1 -g -no-ip -traceback
+
+ #C_COMP=icc
+ C_COMP=mpicc
+ C_OPTS=-O3 -DUNDERSCORE -DLITTLE
+
+ NCARG_DIR=/util/opt/NCL/6.1/lib
+ LIBNCARG=-L$(NCARG_DIR) -lncarg -lncarg_gks -lncarg_c \
+ -L/usr/lib64 -lX11 -ldl -lpng -lpthread -lgfortran -lcairo
+
+ HDF5_LIBS=-L/util/opt/hdf5/1.8/openmpi/1.10/intel/15/lib
+ HDF5_INCS=-I/util/opt/hdf5/1.8/openmpi/1.10/intel/15/include
+
+ NETCDF_LIBS=-L/util/opt/netcdf/4.4/intel/15/lib -lnetcdf
+ NETCDF_INCS=-I/util/opt/netcdf/4.4/intel/15/include
+
+ LOADER=$(F_COMP)
+ LOADER_OPTS=-static-intel $(F_OPTS)
+
+ # For Apple OSX: the stack size needs to be increased at link time
+ # LOADER_OPTS=-static-intel $(F_OPTS) -Wl,-stack_size -Wl,0x10000000
+
+ # to allow ifort compiler to link with pg-compiled ncar graphics:
+ # LIBS=-z muldefs -L/opt/pgi/linux86-64/5.2/lib -lpgftnrtl -lpgc
+
+ ## IMPORTANT: Need to specify this flag in ED2
+ USE_HDF5=1
+ ```
+
+3. <span style="color: rgb(33,33,33);">Command: "**make clean**"</span>
+4. <span style="color: rgb(33,33,33);">Command: "**make -j 8**"</span>
+
+
+
+
+
+
+
+**<span style="color: rgb(51,102,255);">Sample SLURM submit
+scripts</span>**
+
+<span style="color: rgb(51,102,255);">**PGI compiler:**</span>
+
+``` syntaxhighlighter-pre
+#!/bin/sh
+#SBATCH --ntasks=8 # 8 cores
+#SBATCH --mem-per-cpu=1024 # Minimum memory required per CPU (in megabytes)
+#SBATCH --time=03:15:00 # Run time in hh:mm:ss
+#SBATCH --error=/work/[groupname]/[username]/job.%J.err
+#SBATCH --output=/work/[groupname]/[username]/job.%J.out
+
+module load compiler/pgi/11 openmpi/1.6 szip/2.1 zlib/1.2
+
+mpirun /path/to/olam-4.2c-mpi
+```
+
+**<span style="color: rgb(51,102,255);">
+</span>**
+
+<span style="color: rgb(51,102,255);">**Intel compiler:**</span>
+
+``` syntaxhighlighter-pre
+#!/bin/sh
+#SBATCH --ntasks=8 # 8 cores
+#SBATCH --mem-per-cpu=1024 # Minimum memory required per CPU (in megabytes)
+#SBATCH --time=03:15:00 # Run time in hh:mm:ss
+#SBATCH --error=/work/[groupname]/[username]/job.%J.err
+#SBATCH --output=/work/[groupname]/[username]/job.%J.out
+
+module load compiler/intel/12 openmpi/1.6 szip/2.1 zlib/1.2
+
+mpirun /path/to/olam-4.2c-mpi
+```
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/8127343.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/8127413.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/8127668.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/8127744.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/8945698.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/8945732.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/8945791.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/8945826.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/8945860.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/8945894.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/8945946.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/8946016.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/9863202.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/9863236.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/9863288.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/9863363.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/9863419.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/9863456.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/9863555.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/9863657.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/9863714.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/9863798.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/9863850.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/9863911.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/10387512.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/10944561.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/10944601.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11632799.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11632887.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11632937.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11633012.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11633089.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11633159.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11633238.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11633289.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11633379.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11633442.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11633482.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11633556.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11633641.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11633682.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11633729.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11633769.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11633872.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11633936.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11633976.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11634024.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11634066.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11634106.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11634155.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11634203.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11634297.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11634431.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11634534.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11634597.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11634675.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11634725.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11634923.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11635004.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11635127.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11635232.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11635416.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11635682.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11635776.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11635824.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11635866.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11635908.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11635950.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11636037.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11636140.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11636192.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11636303.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11636359.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11636446.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11636552.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11636598.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11636666.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11636809.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11636890.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11636934.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11637108.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11637177.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11637631.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11637675.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11637915.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11638006.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11638081.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11638151.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/11638194.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/12550237.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/12550285.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/12550335.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/13041746.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/13041834.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/13041906.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/13041968.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/13042124.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/13042248.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/13042297.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/13042340.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/13042443.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/13042513.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/13042610.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/13042656.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/13598780.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/13599002.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/13599357.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/13599413.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+[tusker\_modules.xml](attachments/8192234/35324608.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/35325630.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/8192234/35325743.xml)
+(application/octet-stream)
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+[tusker\_modules.xml](attachments/8192234/8127246.xml)
+(application/octet-stream)
+
+Document generated by Confluence on Oct 24, 2018 14:54
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/running_theano.md b/content/guides/running_applications/running_theano.md
new file mode 100644
index 00000000..a7863611
--- /dev/null
+++ b/content/guides/running_applications/running_theano.md
@@ -0,0 +1,105 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Running Applications](Running-Applications_7471153.html)
+
+<span id="title-text"> HCC-DOCS : Running Theano </span>
+========================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified on
+Jun 14, 2018
+
+Theano is available on HCC resources via the modules system. CPU
+versions are available on Sandhills and Tusker; both CPU and GPU
+versions are available on Crane. Additionally, installs for both Python
+2.7 and 3.6 are provided.
+
+### Initial Setup
+
+Theano attempts to write to a `~/.theano` directory in some
+circumstances, which can cause errors as the `/home` filesystem is
+read-only on HCC machines. As a workaround, create the directory on
+`/work` and make a symlink from `/home`:
+
+**Create & symlink .theano directory**
+
+``` syntaxhighlighter-pre
+mkdir -p $WORK/.theano
+ln -s $WORK/.theano $HOME/.theano
+```
+
+This only needs to be done once on each HCC machine.
+
+### Running the CPU version
+
+To use the CPU version, simply load the module and run your Python code.
+ You can choose between the Python 2.7, 3.5 or 3.6 environments:
+
+**Python 2.7 version**
+
+``` syntaxhighlighter-pre
+module load theano/py27/1.0
+python my_python2_script.py
+```
+
+or
+
+**Python 3.5 version**
+
+``` syntaxhighlighter-pre
+module load theano/py35/1.0
+python my_python3_script.py
+```
+
+or
+
+**Python 3.6 version**
+
+``` syntaxhighlighter-pre
+module load theano/py36/1.0
+python my_python3_script.py
+```
+
+<span style="color: rgb(0,0,0);font-size: 16.0px;font-weight: bold;">
+</span>
+
+<span
+style="color: rgb(0,0,0);font-size: 16.0px;font-weight: bold;">Running
+the GPU version</span>
+
+To use the GPU version, first create a `~/.theanorc` file with the
+following contents (or append to an existing file as needed):
+
+**\~/.theanorc**
+
+``` syntaxhighlighter-pre
+[global]
+device = cuda
+```
+
+Next, load the theano module:
+
+**Load the theano module**
+
+``` syntaxhighlighter-pre
+module load theano/py27/0.9
+```
+
+To test the GPU support, start an interactive job on a GPU node and
+import the theano module within the Python interpreter. You should see
+output similar to the following:
+
+**GPU support test**
+
+``` syntaxhighlighter-pre
+Python 2.7.15 | packaged by conda-forge | (default, May 8 2018, 14:46:53)
+[GCC 4.8.2 20140120 (Red Hat 4.8.2-15)] on linux2
+Type "help", "copyright", "credits" or "license" for more information.
+>>> import theano
+Using cuDNN version 7005 on context None
+Mapped name None to device cuda: Tesla K20m (0000:03:00.0)
+```
+
+Document generated by Confluence on Oct 24, 2018 14:54
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/using_anaconda_package_manager.md b/content/guides/running_applications/using_anaconda_package_manager.md
new file mode 100644
index 00000000..98461b13
--- /dev/null
+++ b/content/guides/running_applications/using_anaconda_package_manager.md
@@ -0,0 +1,289 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Running Applications](Running-Applications_7471153.html)
+
+<span id="title-text"> HCC-DOCS : Using Anaconda Package Manager </span>
+========================================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified by
+<span class="editor"> Carrie Brown</span> on Oct 01, 2018
+
+<a href="https://www.anaconda.com/what-is-anaconda/" class="external-link">Anaconda</a>,
+from <a href="http://www.continuum.io" class="external-link">Continuum Analytics</a>
+is a completely free enterprise-ready distribution for large-scale data
+processing, predictive analytics, and scientific computing. It includes
+over 195 of the most popular Python packages for science, math,
+engineering, and data analysis. **It also offers the ability to easily
+create custom *environments* by mixing and matching different versions
+of Python and/or R and other packages into isolated environments that
+individual users are free to create.** Anaconda includes the `conda`
+package and environment manager to make managing these environments
+straightforward.
+
+- [Using Anaconda](#UsingAnacondaPackageManager-UsingAnaconda)
+- [Installing
+ Packages](#UsingAnacondaPackageManager-InstallingPackages)
+- [Adding Packages to an Existing
+ Environment](#UsingAnacondaPackageManager-AddingPackagestoanExistingEnvironment)
+- [Using an Anaconda Environment in a Jupyter Notebook on
+ Crane](#UsingAnacondaPackageManager-UsinganAnacondaEnvironmentinaJupyterNotebookonCrane)
+
+Using Anaconda
+--------------
+
+While the standard methods of installing packages via `pip`
+and `easy_install` work with Anaconda, the preferred method is using
+the `conda` command.
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-warning confluence-information-macro-icon"></span>
+
+Full documentation on using Conda is available
+at <a href="http://conda.pydata.org/docs/" class="external-link">http://conda.pydata.org/docs/</a>
+
+A [cheatsheet](attachments/11635088/11635089.pdf) is also provided.
+
+A few examples of the basic commands are provided here. For a full
+explanation of all of Anaconda/Conda's capabilities, see the
+documentation linked above.
+
+Anaconda is provided through the `anaconda` module on HCC machines. To
+begin using it, load the Anaconda module.
+
+**Load the Anaconda module to start using Conda**
+
+``` syntaxhighlighter-pre
+module load anaconda
+```
+
+<span style="line-height: 1.4285715;">To display general information
+about Conda/Anaconda, use the </span>`info `<span
+style="line-height: 1.4285715;">subcommand.</span>
+
+**Display general information about Conda/Anaconda**
+
+``` syntaxhighlighter-pre
+conda info
+```
+
+Conda allows the easy creation of isolated, custom environments with
+packages and versions of your choosing. To show all currently available
+environments, and which is active, use the `info `subcommand with the
+`-e` option.
+
+**List available environments**
+
+``` syntaxhighlighter-pre
+conda info -e
+```
+
+The active environment will be marked with an asterisk (\*) character.
+
+<span style="line-height: 1.4285715;">The </span>`list `<span
+style="line-height: 1.4285715;">command will show all packages installed
+in the currently active environment.</span>
+
+**List installed packages in current environment**
+
+``` syntaxhighlighter-pre
+conda list
+```
+
+Installing Packages
+-------------------
+
+To find the names of packages, use the `search `subcommand.
+
+**Search for packages**
+
+``` syntaxhighlighter-pre
+conda search numpy
+```
+
+If the package is available, this will also display available package
+versions and compatible Python versions the package may be installed
+under.
+
+The `create` command is used to create a new environment. It requires
+at a minimum a name for the environment, and at least one package to
+install. For example, suppose we wish to create a new environment, and
+need version 1.8 of NumPy.
+
+**Create a new environment by providing a name and package
+specification**
+
+``` syntaxhighlighter-pre
+conda create -n mynumpy numpy=1.8
+```
+
+This will create a new environment called 'mynumpy' and installed NumPy
+version 1.8, along with any required dependencies.
+
+To use the environment, we must first *activate *it.
+
+**Activate environment**
+
+``` syntaxhighlighter-pre
+source activate mynumpy
+```
+
+Our new environment is now active, and we can use it. The shell prompt
+will change to indicate this as well (this can be disable if desired).
+
+Adding Packages to an Existing Environment
+------------------------------------------
+
+To install additional packages in an environment, use the `install`
+subcommand. Suppose we want to install iPython in our 'mynumpy'
+environment. While the environment is active, use `install `with no
+additional arguments.
+
+**Install a new package in the currently active environment**
+
+``` syntaxhighlighter-pre
+conda install ipython
+```
+
+If you aren't currently in the environment you wish to install the
+package in, add the `-n `option to specify the name.
+
+**Install new packages in a specified environment**
+
+``` syntaxhighlighter-pre
+conda install -n mynumpy ipython
+```
+
+<span class="inline-comment-marker"
+data-ref="ca5bc320-0176-45f6-8985-80640d74b744">The </span>`remove `<span
+class="inline-comment-marker"
+data-ref="ca5bc320-0176-45f6-8985-80640d74b744">subcommand to uninstall
+a package functions similarly.</span>
+
+**Remove package from currently active environment**
+
+``` syntaxhighlighter-pre
+conda remove ipython
+```
+
+**Remove package from environment specified by name**
+
+``` syntaxhighlighter-pre
+conda remove -n mynumpy ipython
+```
+
+To exit an environment, we *deactivate *it.
+
+**Exit current environment**
+
+``` syntaxhighlighter-pre
+source deactivate
+```
+
+Finally, to completely remove an environment, add the `--all `option
+to `remove`.
+
+**Completely remove an environment**
+
+``` syntaxhighlighter-pre
+conda remove -n mynumpy --all
+```
+
+Using an Anaconda Environment in a Jupyter Notebook on Crane
+------------------------------------------------------------
+
+It is not difficult to make an Anaconda environment available to a
+Jupyter Notebook. To do so, follow the steps below, replacing <span
+class="underline">myenv</span> with the name of the Python or R
+environment you wish to use:
+
+1. Stop any running Jupyter Notebooks and ensure you are logged out of
+ the JupyterHub instance at
+ <a href="http://crane.unl.edu" class="external-link">http://crane.unl.edu</a>
+ 1. If you are not logged out, please click the Control Panel button
+ located in the top right corner.
+ 2. Click the "Stop My Server" Button to terminate the Jupyter
+ server.
+ 3. Click the logout button in the top right corner.
+
+2. Using the command-line environment, load the target conda
+ environment:
+
+ ``` syntaxhighlighter-pre
+ source activate myenv
+ ```
+
+3. Install the Jupyter kernel and add the environment:
+
+ 1. For a **Python** conda environment, install the IPykernel
+ package, and then the kernel specification:
+
+ ``` syntaxhighlighter-pre
+ # Install ipykernel
+ conda install ipykernel
+
+ # Install the kernel specification
+ python -m ipykernel install --user --name "$CONDA_DEFAULT_ENV" --display-name "Python ($CONDA_DEFAULT_ENV)"
+ ```
+
+ 2. For an **R** conda environment, install the jupyter\_client and
+ IRkernel packages, and then the kernel specification:
+
+ ``` syntaxhighlighter-pre
+ # Install PNG support for R, the R kernel for Jupyter, and the Jupyter client
+ conda install r-png
+ conda install r-irkernel jupyter_client
+
+ # Install jupyter_client 5.2.3 from anaconda channel for bug workaround
+ conda install -c anaconda jupyter_client
+
+ # Install the kernel specification
+ R -e "IRkernel::installspec(name = '$CONDA_DEFAULT_ENV', displayname = 'R ($CONDA_DEFAULT_ENV)', user = TRUE)"
+ ```
+
+4. Once you have the environment set up, deactivate it:
+
+ ``` syntaxhighlighter-pre
+ source deactivate
+ ```
+
+5. To make your conda environments accessible from the worker nodes,
+ enter the following commands:
+
+ ``` syntaxhighlighter-pre
+ mkdir -p $WORK/.jupyter
+ mv ~/.local/share/jupyter/kernels $WORK/.jupyter
+ ln -s $WORK/.jupyter/kernels ~/.local/share/jupyter/kernels
+ ```
+
+ <span
+ class="aui-icon aui-icon-small aui-iconfont-info confluence-information-macro-icon"></span>
+ Note: Step 5 only needs to be done once. Any future created
+ environments will automatically be accessible from SLURM notebooks
+ once this is done.
+
+6. Login to JupyterHub at
+ <a href="http://crane.unl.edu" class="external-link">http://crane.unl.edu</a>
+ and create a new notebook using the environment by selecting the
+ correct entry in the \`New\` dropdown menu in the top right
+ corner.
+
+ <span
+ class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/11635088/24151931.png" class="confluence-embedded-image image-center" height="400" /></span>
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[conda-cheatsheet.pdf](attachments/11635088/11635089.pdf)
+(application/pdf)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2017-11-1\_14-35-48.png](attachments/11635088/24151930.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2017-11-1\_14-37-9.png](attachments/11635088/24151931.png)
+(image/png)
+
+Document generated by Confluence on Oct 24, 2018 14:54
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/running_applications/using_singularity.md b/content/guides/running_applications/using_singularity.md
new file mode 100644
index 00000000..915b60e5
--- /dev/null
+++ b/content/guides/running_applications/using_singularity.md
@@ -0,0 +1,325 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Running Applications](Running-Applications_7471153.html)
+
+<span id="title-text"> HCC-DOCS : Using Singularity </span>
+===========================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified on
+Apr 17, 2018
+
+<a href="http://singularity.lbl.gov" class="external-link">Singularity</a>
+is a containerization solution designed for high-performance computing
+cluster environments. It allows a user on an HPC resource to run an
+application using a different operating system than the one provided by
+the cluster. For example, the application may require Ubuntu but the
+cluster OS is CentOS. Conceptually, it is similar to other container
+software such as Docker, but is designed with several important
+differences that make it more suited for HPC environments.
+
+- Encapsulation of the environment
+- Containers are image based
+- No user contextual changes or root escalation allowed
+- No root owned daemon processes
+
+To use Singularity on HCC machines, first load the `singularity `module.
+ Singularity provides a few different ways to access the container.
+ Most common is to use the `exec` command to run a specific command
+within the container; alternatively, the `shell` command is used to
+launch a bash shell and work interactively. Both commands take the
+source of the image to run as the first argument. The `exec` command
+takes an additional argument for the command within the container to
+run. Singularity can run images from a variety of sources, including
+both a flat image file or a Docker image from Docker Hub. For
+convenience, HCC provides a set of images on
+<a href="https://hub.docker.com/u/unlhcc/dashboard/" class="external-link">Docker Hub</a>
+known to work on HCC resources. Finally, pass any arguments for the
+program itself in the same manner as you would if running it directly.
+ For example, the Spades Assembler software is run using the Docker
+image <span style="font-family: monospace;">unlhcc/spades</span> and via
+the command `spades.py`. To run the software using Singularity, the
+commands are:
+
+**Run Spades using Singularity**
+
+``` syntaxhighlighter-pre
+module load singularity
+singularity exec docker://unlhcc/spades spades.py <spades arguments>
+```
+
+Using Singularity in a SLURM job is the same as any other software.
+
+**Example Singularity SLURM script**
+
+``` syntaxhighlighter-pre
+#!/bin/sh
+#SBATCH --time=03:15:00 # Run time in hh:mm:ss
+#SBATCH --mem-per-cpu=4096 # Maximum memory required per CPU (in megabytes)
+#SBATCH --job-name=singularity-test
+#SBATCH --error=/work/[groupname]/[username]/job.%J.err
+#SBATCH --output=/work/[groupname]/[username]/job.%J.out
+
+module load singularity
+singularity exec docker://unlhcc/spades spades.py <spades arguments>
+```
+
+### Available Images
+
+The following table lists the currently available images and the command
+to run the software.
+
+Request additional images
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-warning confluence-information-macro-icon"></span>
+
+If you would like to request an image to be added, please fill out the
+HCC
+<a href="http://hcc.unl.edu/software-installation-request" class="external-link">Software Request Form</a>
+and indicate you would like to use Singularity.
+
+| Software | Version | Command to Run | Additional Notes |
+|--------------------------------|----------------|-----------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------|
+| DREAM3D | 6.3.29, 6.5.36 | `singularity exec docker://unlhcc/dream3d PipelineRunner` | |
+| Spades | 3.11.0 | `singularity exec docker://unlhcc/spades spades.py` | |
+| Macaulay2 | 1.9.2 | `singularity exec docker://unlhcc/macaulay2 M2` | |
+| CUDA (Ubuntu) | 8.0 | `singularity exec docker://unlhcc/cuda-ubuntu <my CUDA program>` | Ubuntu 16.04.1 LTS w/CUDA 8.0 |
+| TensorFlow GPU | 1.4 | `singularity exec docker://unlhcc/tensorflow-gpu python /path/to/my_tf_code.py` | Use `python3` for Python3 code |
+| Keras w/Tensorflow GPU backend | 2.0.4, 2.1.5 | `singularity exec docker://unlhcc/keras-tensorflow-gpu python /path/to/my_keras_code.py` | Use `python3` for Python3 code |
+| Octave | 4.2.1 | `singularity exec docker://unlhcc/octave octave` | |
+| Sonnet GPU | 1.13 | `singularity exec docker://unlhcc/sonnet-gpu python /path/to/my_sonnet_code.py` | Use `python3` for Python3 code |
+| Neurodocker w/ANTs | 2.2.0 | `singularity exec docker://unlhcc/neurodocker-ants <ants script>` | Replace `<ants script>` with the desired ANTs program |
+| GNU Radio | 3.7.11 | `singularity exec docker://unlhcc/gnuradio python /path/to/my_gnuradio_code.py` | Replace `python /path/to/my_gnuradio_code.py` with other GNU Radio commands to run |
+| Neurodocker w/AFNI | 17.3.00 | `singularity exec docker://unlhcc/neurodocker-afni <AFNI program>` | Replace `<AFNI program>` with the desired AFNI program |
+| Neurodocker w/FreeSurfer | 6.0.0 | `singularity run -B <path to your FS license>:/opt/freesurfer/license.txt docker://unlhcc/neurodocker-freesurfer recon-all` | Substitute `<path to your FS license>` with the full path to your particular FS license file. Replace `recon-all` with other FreeSurfer commands to run. |
+| fMRIprep | 1.0.7 | `singularity exec docker://unlhcc/fmriprep fmriprep` | |
+| ndmg | 0.0.50 | `singularity exec docker://unlhcc/ndmg ndmg_bids` | |
+| NIPYPE (Python2) | 1.0.0 | `singularity exec docker://unlhcc/nipype-py27 <NIPYPE program>` | Replace `<NIPYPE program>` with the desired NIPYPE program |
+| NIPYPE (Python3) | 1.0.0 | `singularity exec docker://unlhcc/nipype-py36 <NIPYPE program>` | Replace `<NIPYPE program>` with the desired NIPYPE program |
+| DPARSF | 4.3.12 | `singularity exec docker://unlhcc/dparsf <DPARSF program>` | Replace `<DPARSF program>` with the desired DPARSF program |
+| Caffe GPU | 1.0 | `singularity exec docker://unlhcc/caffe-gpu caffe` | |
+| ENet Caffe GPU | 427a014 | `singularity exec docker://unlhcc/enet-caffe-gpu <ENET program>` | Replace `<ENET program>` with the desired ENET program |
+| ROS Kinetic | 1.3.1 | `singularity exec docker://unlhcc/ros-kinetic <ROS program>` | Replace `<ROS program>` with the desired ROS program |
+| Mitsuba | 1.5.0 | `singularity exec docker://unlhcc/mitsuba mitsuba` | |
+| FImpute | 2.2 | `singularity exec docker://unlhcc/fimpute FImpute <control file>` | Replace `<control file>` with the control file you have prepared |
+| Neurodocker w/FSL | 5.0.11 | `singularity run docker://unlhcc/neurodocker-fsl <FSL program>` | Replace `<FSL program>` with the desired FSL program. This image includes GPU support. |
+
+### What if I need other Python packages not in the image?
+
+Unfortunately it's not possible to create one image that has every
+available Python package installed for logistical reasons. Images are
+created with a small set of the most commonly-used scientific packages,
+but you may need others. If so, you can install them in a location in
+your `$WORK` directory and set the `PYTHONPATH` variable to that
+location in your submit script. The extra packages will then be "seen"
+by the Python interpreter within the image. To ensure the packages will
+work, the install must be done from within the container via
+the `singularity shell` command. For example, suppose you are using
+the `tensorflow-gpu` image and need the packages `nibabel` and `tables`.
+ First, run an interactive SLURM job to get a shell on a worker node.
+
+**Run an interactive SLURM job**
+
+``` syntaxhighlighter-pre
+srun --pty --mem=4gb --qos=short $SHELL
+```
+
+After the job starts, the prompt will change to indicate you're on a
+worker node. Next, start an interactive session in the container.
+
+**Start a shell in the container**
+
+``` syntaxhighlighter-pre
+module load singularity
+singularity shell docker://unlhcc/tensorflow-gpu
+```
+
+This may take a few minutes to start. Again, the prompt will change and
+begin with `Singularity` to indicate you're within the container.
+
+Next, install the needed packages via `pip` to a location somewhere in
+your `work` directory. For example, `$WORK/tf-gpu-pkgs`. (If you are
+using Python 3, use `pip3` instead of `pip`).
+
+**Install needed Python packages with pip**
+
+``` syntaxhighlighter-pre
+export LC_ALL=C
+pip install --system --target=$WORK/tf-gpu-pkgs --install-option="--install-scripts=$WORK/tf-gpu-pkgs/bin" nibabel tables
+```
+
+You should see some progress indicators, and a
+"`Successfully installed..."` message at the end. Exit both the
+container and the interactive SLURM job by typing `exit` twice. The
+above steps only need to be done once per each image you need additional
+packages for. Be sure to use a separate location for each image's
+extra packages.
+
+To make the packages visible within the container, you'll need to add a
+line to the submit script used for your Singularity job. Before the
+lines to load the `singularity `module and run the script, add a line
+setting the `PYTHONPATH` variable to the `$WORK/tf-gpu-pkgs` directory.
+ For example,
+
+**Example SLURM script**
+
+``` syntaxhighlighter-pre
+#!/bin/sh
+#SBATCH --time=03:15:00 # Run time in hh:mm:ss
+#SBATCH --mem-per-cpu=4096 # Maximum memory required per CPU (in megabytes)
+#SBATCH --job-name=singularity-test
+#SBATCH --partition=gpu
+#SBATCH --gres=gpu
+#SBATCH --error=/work/[groupname]/[username]/job.%J.err
+#SBATCH --output=/work/[groupname]/[username]/job.%J.out
+
+export PYTHONPATH=$WORK/tf-gpu-pkgs
+module load singularity
+singularity exec docker://unlhcc/tensorflow-gpu python /path/to/my_tf_code.py
+```
+
+The additional packages should then be available for use by your Python
+code running within the container.
+
+### What if I need a specific software version of the Singularity image?
+
+You can see all the available versions of the software built with
+Singularity in the table above. If you don't specify a specific sofware
+version, Singulariy will use the latest one. If you want to use a
+specific version instead, you can append the version number from the
+table to the image. For example, if you want to use the Singularity
+image for Spades version 3.11.0, type:
+
+``` syntaxhighlighter-pre
+singularity exec docker://unlhcc/spades:3.11.0 spades.py
+```
+
+### What if I want to build a custom image to use on the HCC clusters?
+
+<span style="color: rgb(0,0,0);">You can create custom Docker image and
+use it with Singularity on our clusters. Singularity can run images
+directly from Docker Hub, so you don't need to upload anything to HCC.
+For this purpose, you just need to have a Docker Hub account and upload
+your image there. Then, if you want to run the command "*mycommand*"
+from the image "*myimage*", type:</span>
+
+``` syntaxhighlighter-pre
+module load singularity
+singularity exec docker://myaccount/myimage mycommand
+```
+
+<span style="color: rgb(0,0,0);">where "*myaccount*" is your Docker Hub
+account.</span>
+
+<span style="color: rgb(0,0,0);">In case you see the error "<span
+style="color: rgb(153,51,102);">ERROR MANIFEST\_INVALID: manifest
+invalid</span>" when running the command above, try:</span>
+
+``` syntaxhighlighter-pre
+module load singularity
+unset REGISTRY
+singularity exec docker://myaccount/myimage mycommand
+```
+
+<span style="color: rgb(0,0,0);">All the Dockerfiles of the images we
+host on HCC are
+<a href="https://github.com/unlhcc/singularity-dockerfiles" class="external-link">publicly available here</a></span><span
+style="color: rgb(0,0,0);">. You can use them as an example when
+creating your own image. The only thing you need to note w</span><span
+style="color: rgb(0,0,0);">hen creating custom Docker images you want to
+use on HCC is to add the line:
+</span>`RUN mkdir -p /work`<span style="color: rgb(0,0,0);">at the end
+of your Dockerfile. This creates a "</span>*/work*<span
+style="color: rgb(0,0,0);">" directory inside your image so your
+"</span>*/work*<span style="color: rgb(0,0,0);">" directory on
+Crane/Tusker is available.</span>
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[IMAGELIST.md](attachments/17040488/17041276.md)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[IMAGELIST.md](attachments/17040488/17043291.md)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[IMAGELIST.md](attachments/17040488/18548329.md)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[IMAGELIST.md](attachments/17040488/21071161.md)
+(application/octet-stream)
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+(application/octet-stream)
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+(application/octet-stream)
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+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[IMAGELIST.md](attachments/17040488/24151704.md)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[IMAGELIST.md](attachments/17040488/24151705.md)
+(application/octet-stream)
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+[IMAGELIST.md](attachments/17040488/24152060.md)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[IMAGELIST.md](attachments/17040488/24152061.md)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[IMAGELIST.md](attachments/17040488/24152145.md)
+(application/octet-stream)
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+[IMAGELIST.md](attachments/17040488/30444516.md)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[IMAGELIST.md](attachments/17040488/30444517.md)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[IMAGELIST.md](attachments/17040488/30446691.md)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[IMAGELIST.md](attachments/17040488/33685989.md)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[IMAGELIST.md](attachments/17040488/35324359.md)
+(application/octet-stream)
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+[IMAGELIST.md](attachments/17040488/17041272.md)
+(application/octet-stream)
+
+Document generated by Confluence on Oct 24, 2018 14:54
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/submitting_jobs/_index.md b/content/guides/submitting_jobs/_index.md
new file mode 100644
index 00000000..9ad7fcba
--- /dev/null
+++ b/content/guides/submitting_jobs/_index.md
@@ -0,0 +1,228 @@
++++
+title = "Submitting Jobs"
+description = "How to submit jobs to HCC resources"
+weight = "10"
++++
+
+HCC-DOCS : Submitting Jobs
+=========================================================
+
+Crane, Sandhills and Tusker are managed by
+the <a href="https://slurm.schedmd.com" class="external-link">SLURM</a> resource
+manager. In order to run processing on Crane, Sandhills or Tusker, you
+must create a SLURM script that will run your processing. After
+submitting the job, SLURM will schedule your processing on an available
+worker node.
+
+Before writing a submit file, you may need to [compile your
+application](Compiling-Source-Code_332258.html).
+
+- [Ensure proper working directory for job
+ output](#SubmittingJobs-Ensureproperworkingdirectoryforjoboutput)
+- [Creating a SLURM Submit
+ File](#SubmittingJobs-CreatingaSLURMSubmitFile)
+- [Submitting the job](#SubmittingJobs-Submittingthejob)
+- [Checking Job Status](#SubmittingJobs-CheckingJobStatus)
+ - [Checking Job Start](#SubmittingJobs-CheckingJobStart)
+- [Next Steps](#SubmittingJobs-NextSteps)
+
+Ensure proper working directory for job output
+----------------------------------------------
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-warning confluence-information-macro-icon"></span>
+
+All SLURM job output should be directed to your /work path.
+
+**manual specification of /work path**
+
+``` syntaxhighlighter-pre
+$ cd /work/[groupname]/[username]
+```
+
+The environment variable $WORK can also be used.
+
+**using environment for /work path**
+
+``` syntaxhighlighter-pre
+$ cd $WORK
+$ pwd
+/work/[groupname]/[username]
+```
+
+Review how /work differs from /home [here.](Handling-Data_332256.html)
+
+Creating a SLURM Submit File
+----------------------------
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-warning confluence-information-macro-icon"></span>
+
+The below example is for a serial job. For submitting MPI jobs, please
+look at the [MPI Submission Guide.](Submitting-an-MPI-Job_332242.html)
+
+A SLURM submit file is broken into 2 sections, the job description and
+the processing. SLURM job description are prepended with `#SBATCH` in
+the submit file.
+
+**SLURM Submit File**
+
+``` syntaxhighlighter-pre
+#!/bin/sh
+#SBATCH --time=03:15:00 # Run time in hh:mm:ss
+#SBATCH --mem-per-cpu=1024 # Maximum memory required per CPU (in megabytes)
+#SBATCH --job-name=hello-world
+#SBATCH --error=/work/[groupname]/[username]/job.%J.err
+#SBATCH --output=/work/[groupname]/[username]/job.%J.out
+
+module load example/test
+
+hostname
+sleep 60
+```
+
+- **time**
+ Maximum walltime the job can run. After this time has expired, the
+ job will be stopped.
+- **mem-per-cpu**
+ Memory that is allocated per core for the job. If you exceed this
+ memory limit, your job will be stopped.
+- **mem**
+ Specify the real memory required per node in MegaBytes. If you
+ exceed this limit, your job will be stopped. Note that for you
+ should ask for less memory than each node actually has. For
+ instance, Tusker has 1TB, 512GB and 256GB of RAM per node. You may
+ only request 1000GB of RAM for the 1TB node, 500GB of RAM for the
+ 512GB nodes, and 250GB of RAM for the 256GB nodes. For Crane, the
+ max is 500GB.
+- **job-name
+ **The name of the job. Will be reported in the job listing.
+- **partition**
+ The partition the job should run in. Partitions determine the job's
+ priority and on what nodes the partition can run on. See [Available
+ Partitions on
+ Sandhills](Available-Partitions-on-Sandhills_332211.html), and
+ [Available Partitions on Crane and
+ Tusker](https://hcc-docs.unl.edu/display/HCCDOC/Available+Partitions+on+Crane+and+Tusker) for
+ a list of possible partitions.
+- **error**
+ Location of the stderr will be written for the job. `[groupname]`
+ and `[username]` should be replaced your group name and username.
+ Your username can be retrieved with the command `id -un` and your
+ group with `id -ng`.
+- **output**
+ Location of the stdout will be written for the job.
+
+More advanced submit commands can be found on the
+<a href="https://slurm.schedmd.com/sbatch.html" class="external-link">SLURM Docs</a>.
+ You can also find an example of a MPI submission on [Submitting an MPI
+Job](Submitting-an-MPI-Job_332242.html).
+
+Submitting the job
+------------------
+
+Submitting the SLURM job is done by command `sbatch`. SLURM will read
+the submit file, and schedule the job according to the description in
+the submit file.
+
+Submitting the job described above is:
+
+**SLURM Submission**
+
+``` syntaxhighlighter-pre
+$ sbatch example.slurm
+Submitted batch job 24603
+```
+
+The job was successfully submitted.
+
+Checking Job Status
+-------------------
+
+Job status is found with the command `squeue`. It will provide
+information such as:
+
+- The State of the job:
+ - **R** - Running
+ - **PD** - Pending - <span style="color: rgb(0,0,0);">Job is
+ awaiting resource allocation.</span>
+ - <span style="color: rgb(0,0,0);">Additional codes are available
+ on the
+ <a href="http://slurm.schedmd.com/squeue.html" class="external-link">squeue</a>
+ page.</span><span style="color: rgb(0,0,0);">
+ </span>
+- <span style="color: rgb(0,0,0);">Job Name</span>
+- <span style="color: rgb(0,0,0);">Run Time</span>
+- <span style="color: rgb(0,0,0);">Nodes running the job</span>
+
+Checking the status of the job is easiest by filtering by your username,
+using the `-u` option to squeue.
+
+``` syntaxhighlighter-pre
+$ squeue -u <username>
+ JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
+ 24605 batch hello-wo <username> R 0:56 1 b01
+```
+
+Additionally, if you want to see the status of a specific partition, for
+example if you are part of a
+[partition](Available-Partitions-on-Sandhills_332211.html), you can use
+the `-p` option to `squeue`:
+
+``` syntaxhighlighter-pre
+$ squeue -p esquared
+ JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
+ 73435 esquared MyRandom tingting R 10:35:20 1 ri19n10
+ 73436 esquared MyRandom tingting R 10:35:20 1 ri19n12
+ 73735 esquared SW2_driv hroehr R 10:14:11 1 ri20n07
+ 73736 esquared SW2_driv hroehr R 10:14:11 1 ri20n07
+```
+
+### Checking Job Start
+
+You may view the start time of your job with the
+command `squeue --start`. The output of the command will show the
+expected start time of the jobs.
+
+``` syntaxhighlighter-pre
+$ squeue --start --user lypeng
+ JOBID PARTITION NAME USER ST START_TIME NODES NODELIST(REASON)
+ 5822 batch Starace lypeng PD 2013-06-08T00:05:09 3 (Priority)
+ 5823 batch Starace lypeng PD 2013-06-08T00:07:39 3 (Priority)
+ 5824 batch Starace lypeng PD 2013-06-08T00:09:09 3 (Priority)
+ 5825 batch Starace lypeng PD 2013-06-08T00:12:09 3 (Priority)
+ 5826 batch Starace lypeng PD 2013-06-08T00:12:39 3 (Priority)
+ 5827 batch Starace lypeng PD 2013-06-08T00:12:39 3 (Priority)
+ 5828 batch Starace lypeng PD 2013-06-08T00:12:39 3 (Priority)
+ 5829 batch Starace lypeng PD 2013-06-08T00:13:09 3 (Priority)
+ 5830 batch Starace lypeng PD 2013-06-08T00:13:09 3 (Priority)
+ 5831 batch Starace lypeng PD 2013-06-08T00:14:09 3 (Priority)
+ 5832 batch Starace lypeng PD N/A 3 (Priority)
+```
+
+The output shows the expected start time of the jobs, as well as the
+reason that the jobs are currently idle (in this case, low priority of
+the user due to running numerous jobs already).
+
+
+
+<span
+style="color: rgb(0,0,0);font-size: 20.0px;line-height: 1.5;">Removing
+the Job</span>
+
+Removing the job is done with the `scancel` command. The only argument
+to the `scancel` command is the job id. For the job above, the command
+is:
+
+``` syntaxhighlighter-pre
+$ scancel 24605
+```
+
+Next Steps
+----------
+
+
+
+Document generated by Confluence on Oct 24, 2018 14:47
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/submitting_jobs/available_partitions_on_crane_and_tusker.md b/content/guides/submitting_jobs/available_partitions_on_crane_and_tusker.md
new file mode 100644
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--- /dev/null
+++ b/content/guides/submitting_jobs/available_partitions_on_crane_and_tusker.md
@@ -0,0 +1,623 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Submitting Jobs](Submitting-Jobs_332222.html)
+
+<span id="title-text"> HCC-DOCS : Available Partitions on Crane and Tusker </span>
+==================================================================================
+
+Created by <span class="author"> John Thiltges</span>, last modified by
+<span class="editor"> Adam Caprez</span> on Sep 14, 2018
+
+Partitions are used in Crane and Tusker to distinguish different
+resources. You can view the partitions with the command `sinfo`.
+
+Crane:
+------
+
+*last generated Wed Oct 24 14:47:56 2018*
+
+<table style="width:100%;">
+<colgroup>
+<col style="width: 8%" />
+<col style="width: 11%" />
+<col style="width: 18%" />
+<col style="width: 18%" />
+<col style="width: 19%" />
+<col style="width: 7%" />
+<col style="width: 7%" />
+<col style="width: 7%" />
+</colgroup>
+<thead>
+<tr class="header">
+<th>Partition</th>
+<th>Owner</th>
+<th>Node total (NODExCPU/MEM/FEATURE)</th>
+<th>Description</th>
+<th>SLURM Specification</th>
+<th style="text-align: center;">Max Job Run Time</th>
+<th style="text-align: center;">Max CPUs Per User</th>
+<th style="text-align: center;">Max Jobs Per User</th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td>batch</td>
+<td>shared</td>
+<td>404 total (6x36/256GB/opa; 382x16/64GB/ib; 16x36/512GB/opa)</td>
+<td>(default, no specification)</td>
+<td>#SBATCH --partition=batch</td>
+<td style="text-align: center;">7-00:00:00</td>
+<td style="text-align: center;">ib:2000 opa:576</td>
+<td style="text-align: center;">1000</td>
+</tr>
+<tr class="even">
+<td>guest</td>
+<td>shared</td>
+<td>151 total (73x36/256GB/opa; 20x36/512GB/opa; 58x16/64GB/ib)</td>
+<td>Preemtable partition with ib or opa</td>
+<td>#SBATCH --partition=guest</td>
+<td style="text-align: center;">7-00:00:00</td>
+<td style="text-align: center;">ib:928 opa:2000</td>
+<td style="text-align: center;">1000</td>
+</tr>
+<tr class="odd">
+<td>alexandrov</td>
+<td>alexandrov</td>
+<td>32 total (32x16/64GB/ib)</td>
+<td>Dedicated resources with ib</td>
+<td>#SBATCH --partition=alexandrov</td>
+<td style="text-align: center;">7-00:00:00</td>
+<td style="text-align: center;">ib:512</td>
+<td style="text-align: center;">1000</td>
+</tr>
+<tr class="even">
+<td>tmp_anvil</td>
+<td>shared</td>
+<td>21 total (21x20/256GB/none)</td>
+<td>Shared resources</td>
+<td>#SBATCH --partition=tmp_anvil</td>
+<td style="text-align: center;">7-00:00:00</td>
+<td style="text-align: center;">420</td>
+<td style="text-align: center;">1000</td>
+</tr>
+<tr class="odd">
+<td>gfcluster</td>
+<td>gladich francisco</td>
+<td>20 total (10x36/256GB/opa; 10x36/512GB/opa)</td>
+<td>Dedicated resources with opa</td>
+<td>#SBATCH --partition=gfcluster</td>
+<td style="text-align: center;">7-00:00:00</td>
+<td style="text-align: center;">opa:360</td>
+<td style="text-align: center;">1000</td>
+</tr>
+<tr class="even">
+<td>zeng</td>
+<td>zeng</td>
+<td>16 total (14x36/256GB/opa; 2x36/512GB/opa)</td>
+<td>Dedicated resources with opa</td>
+<td>#SBATCH --partition=zeng</td>
+<td style="text-align: center;">7-00:00:00</td>
+<td style="text-align: center;">opa:504</td>
+<td style="text-align: center;">1000</td>
+</tr>
+<tr class="odd">
+<td>tsymbal</td>
+<td>tsymbal</td>
+<td>14 total (14x36/256GB/opa)</td>
+<td>Dedicated resources with opa</td>
+<td>#SBATCH --partition=tsymbal</td>
+<td style="text-align: center;">7-00:00:00</td>
+<td style="text-align: center;">opa:504</td>
+<td style="text-align: center;">1000</td>
+</tr>
+<tr class="even">
+<td>benson</td>
+<td>benson</td>
+<td>12 total (12x36/256GB/opa)</td>
+<td>Dedicated resources with opa</td>
+<td>#SBATCH --partition=benson</td>
+<td style="text-align: center;">7-00:00:00</td>
+<td style="text-align: center;">opa:432</td>
+<td style="text-align: center;">1000</td>
+</tr>
+<tr class="odd">
+<td>gpu</td>
+<td>shared</td>
+<td>11 total (2x24/128GB/ib,gpu_k20; 1x24/120GB/ib,gpu_k20; 1x8/64GB/gpu_k40; 5x16/64GB/gpu_k40; 2x8/64GB/opa,gpu_p100)</td>
+<td>Shared resources with gpu_p100 or gpu_k20 or ib or gpu_k40 or opa</td>
+<td>#SBATCH --partition=gpu</td>
+<td style="text-align: center;">7-00:00:00</td>
+<td style="text-align: center;">ib:48 opa:16</td>
+<td style="text-align: center;">1000</td>
+</tr>
+<tr class="even">
+<td>jclarke</td>
+<td>jclarke schnablelab</td>
+<td>10 total (4x36/256GB/opa; 6x36/512GB/opa)</td>
+<td>Dedicated resources with opa</td>
+<td>#SBATCH --partition=jclarke</td>
+<td style="text-align: center;">7-00:00:00</td>
+<td style="text-align: center;">opa:216</td>
+<td style="text-align: center;">1000</td>
+</tr>
+<tr class="odd">
+<td>gladich</td>
+<td>gladich</td>
+<td>10 total (10x36/256GB/opa)</td>
+<td>Dedicated resources with opa</td>
+<td>#SBATCH --partition=gladich</td>
+<td style="text-align: center;">7-00:00:00</td>
+<td style="text-align: center;">opa:360</td>
+<td style="text-align: center;">1000</td>
+</tr>
+<tr class="even">
+<td>francisco</td>
+<td>francisco</td>
+<td>10 total (10x36/512GB/opa)</td>
+<td>Dedicated resources with opa</td>
+<td>#SBATCH --partition=francisco</td>
+<td style="text-align: center;">7-00:00:00</td>
+<td style="text-align: center;">opa:360</td>
+<td style="text-align: center;">1000</td>
+</tr>
+<tr class="odd">
+<td>ahouston</td>
+<td>ahouston</td>
+<td>9 total (2x16/64GB/ib; 7x36/256GB/opa)</td>
+<td>Dedicated resources with ib or opa</td>
+<td>#SBATCH --partition=ahouston</td>
+<td style="text-align: center;">28-00:00:00</td>
+<td style="text-align: center;">ib:32 opa:252</td>
+<td style="text-align: center;">1000</td>
+</tr>
+<tr class="even">
+<td>scott</td>
+<td>scott vinod samal</td>
+<td>6 total (1x16/15GB/gpu_1060; 3x16/48GB/gpu_k20; 1x8/95GB/gpu_p100; 1x20/256GB/gpu_titanx)</td>
+<td>Dedicated resources with gpu_p100 or gpu_k20 or gpu_1060 or gpu_titanx</td>
+<td>#SBATCH --partition=scott</td>
+<td style="text-align: center;">7-00:00:00</td>
+<td style="text-align: center;">48</td>
+<td style="text-align: center;">1000</td>
+</tr>
+<tr class="odd">
+<td>larios</td>
+<td>larios</td>
+<td>6 total (4x16/64GB/ib; 2x36/256GB/opa)</td>
+<td>Dedicated resources with ib or opa</td>
+<td>#SBATCH --partition=larios</td>
+<td style="text-align: center;">7-00:00:00</td>
+<td style="text-align: center;">ib:64 opa:72</td>
+<td style="text-align: center;">1000</td>
+</tr>
+<tr class="even">
+<td>qinghuilab</td>
+<td>qinghuilab</td>
+<td>5 total (5x8/192GB/gpu_p100)</td>
+<td>Dedicated resources with gpu_p100</td>
+<td>#SBATCH --partition=qinghuilab</td>
+<td style="text-align: center;">7-00:00:00</td>
+<td style="text-align: center;">40</td>
+<td style="text-align: center;">1000</td>
+</tr>
+<tr class="odd">
+<td>choueiry</td>
+<td>choueiry</td>
+<td>4 total (4x36/256GB/opa)</td>
+<td>Dedicated resources with opa</td>
+<td>#SBATCH --partition=choueiry</td>
+<td style="text-align: center;">7-00:00:00</td>
+<td style="text-align: center;">opa:144</td>
+<td style="text-align: center;">1000</td>
+</tr>
+<tr class="even">
+<td>sabirianov</td>
+<td>sabirianov</td>
+<td>4 total (4x16/64GB/ib)</td>
+<td>Dedicated resources with ib</td>
+<td>#SBATCH --partition=sabirianov</td>
+<td style="text-align: center;">7-00:00:00</td>
+<td style="text-align: center;">ib:64</td>
+<td style="text-align: center;">1000</td>
+</tr>
+<tr class="odd">
+<td>jyanglab</td>
+<td>jyanglab</td>
+<td>4 total (4x16/64GB/ib)</td>
+<td>Dedicated resources with ib</td>
+<td>#SBATCH --partition=jyanglab</td>
+<td style="text-align: center;">7-00:00:00</td>
+<td style="text-align: center;">ib:64</td>
+<td style="text-align: center;">1000</td>
+</tr>
+<tr class="even">
+<td>jaturner</td>
+<td>jaturner</td>
+<td>4 total (4x16/64GB/ib)</td>
+<td>Dedicated resources with ib</td>
+<td>#SBATCH --partition=jaturner</td>
+<td style="text-align: center;">7-00:00:00</td>
+<td style="text-align: center;">ib:64</td>
+<td style="text-align: center;">1000</td>
+</tr>
+<tr class="odd">
+<td>riethoven</td>
+<td>riethoven</td>
+<td>3 total (3x36/256GB/opa)</td>
+<td>Dedicated resources with opa</td>
+<td>#SBATCH --partition=riethoven</td>
+<td style="text-align: center;">7-00:00:00</td>
+<td style="text-align: center;">opa:108</td>
+<td style="text-align: center;">1000</td>
+</tr>
+<tr class="even">
+<td>bigweather</td>
+<td>bigweather</td>
+<td>3 total (3x16/64GB/ib)</td>
+<td>Dedicated resources with ib</td>
+<td>#SBATCH --partition=bigweather</td>
+<td style="text-align: center;">7-00:00:00</td>
+<td style="text-align: center;">ib:48</td>
+<td style="text-align: center;">1000</td>
+</tr>
+<tr class="odd">
+<td>starace</td>
+<td>starace</td>
+<td>2 total (1x36/512GB/opa; 1x16/64GB/ib)</td>
+<td>Dedicated resources with ib or opa</td>
+<td>#SBATCH --partition=starace</td>
+<td style="text-align: center;">7-00:00:00</td>
+<td style="text-align: center;">ib:16 opa:36</td>
+<td style="text-align: center;">1000</td>
+</tr>
+<tr class="even">
+<td>stats</td>
+<td>qizhangstat yzstat</td>
+<td>2 total (2x32/256GB/ib)</td>
+<td>Dedicated resources with ib</td>
+<td>#SBATCH --partition=stats</td>
+<td style="text-align: center;">7-00:00:00</td>
+<td style="text-align: center;">ib:64</td>
+<td style="text-align: center;">1000</td>
+</tr>
+<tr class="odd">
+<td>dwyer</td>
+<td>dwyer</td>
+<td>2 total (2x36/256GB/opa)</td>
+<td>Dedicated resources with opa</td>
+<td>#SBATCH --partition=dwyer</td>
+<td style="text-align: center;">7-00:00:00</td>
+<td style="text-align: center;">opa:72</td>
+<td style="text-align: center;">1000</td>
+</tr>
+<tr class="even">
+<td>esquared</td>
+<td>esquared dwyer vuran cohen nimbus</td>
+<td>2 total (2x36/256GB/opa)</td>
+<td>Dedicated resources with opa</td>
+<td>#SBATCH --partition=esquared</td>
+<td style="text-align: center;">7-00:00:00</td>
+<td style="text-align: center;">opa:72</td>
+<td style="text-align: center;">1000</td>
+</tr>
+<tr class="odd">
+<td>unsmgenomics</td>
+<td>unsmgenomics</td>
+<td>1 total (1x20/256GB/none)</td>
+<td>Dedicated resources</td>
+<td>#SBATCH --partition=unsmgenomics</td>
+<td style="text-align: center;">7-00:00:00</td>
+<td style="text-align: center;">20</td>
+<td style="text-align: center;">1000</td>
+</tr>
+<tr class="even">
+<td>statsgeneral</td>
+<td>statsgeneral</td>
+<td>1 total (1x16/64GB/ib)</td>
+<td>Dedicated resources with ib</td>
+<td>#SBATCH --partition=statsgeneral</td>
+<td style="text-align: center;">7-00:00:00</td>
+<td style="text-align: center;">ib:16</td>
+<td style="text-align: center;">1000</td>
+</tr>
+<tr class="odd">
+<td>abg</td>
+<td>anscgenomics rmlewis</td>
+<td>1 total (1x16/64GB/ib)</td>
+<td>Dedicated resources with ib</td>
+<td>#SBATCH --partition=abg</td>
+<td style="text-align: center;">7-00:00:00</td>
+<td style="text-align: center;">ib:16</td>
+<td style="text-align: center;">1000</td>
+</tr>
+<tr class="even">
+<td>juancui</td>
+<td>juancui</td>
+<td>1 total (1x36/512GB/opa)</td>
+<td>Dedicated resources with opa</td>
+<td>#SBATCH --partition=juancui</td>
+<td style="text-align: center;">7-00:00:00</td>
+<td style="text-align: center;">opa:36</td>
+<td style="text-align: center;">1000</td>
+</tr>
+<tr class="odd">
+<td>gpu_v100</td>
+<td></td>
+<td>1 total (1x36/384GB/gpu_v100)</td>
+<td>Dedicated resources with gpu_v100</td>
+<td>#SBATCH --partition=gpu_v100</td>
+<td style="text-align: center;">7-00:00:00</td>
+<td style="text-align: center;">36</td>
+<td style="text-align: center;">1000</td>
+</tr>
+<tr class="even">
+<td>guda</td>
+<td>unmc_cbsb unmc_gudalab</td>
+<td>1 total (1x36/256GB/opa)</td>
+<td>Dedicated resources with opa</td>
+<td>#SBATCH --partition=guda</td>
+<td style="text-align: center;">7-00:00:00</td>
+<td style="text-align: center;">opa:36</td>
+<td style="text-align: center;">1000</td>
+</tr>
+<tr class="odd">
+<td>waterforfood</td>
+<td>waterforfood</td>
+<td>1 total (1x36/512GB/opa)</td>
+<td>Dedicated resources with opa</td>
+<td>#SBATCH --partition=waterforfood</td>
+<td style="text-align: center;">7-00:00:00</td>
+<td style="text-align: center;">opa:36</td>
+<td style="text-align: center;">1000</td>
+</tr>
+<tr class="even">
+<td>npod</td>
+<td>chunglab juancui ramertait samodha unmc_ngs wtp zempleni</td>
+<td>1 total (1x16/64GB/ib)</td>
+<td>Dedicated resources with ib</td>
+<td>#SBATCH --partition=npod</td>
+<td style="text-align: center;">7-00:00:00</td>
+<td style="text-align: center;">ib:16</td>
+<td style="text-align: center;">1000</td>
+</tr>
+<tr class="odd">
+<td>thinklab</td>
+<td>thinklab</td>
+<td>1 total (1x16/64GB/ib)</td>
+<td>Dedicated resources with ib</td>
+<td>#SBATCH --partition=thinklab</td>
+<td style="text-align: center;">7-00:00:00</td>
+<td style="text-align: center;">ib:16</td>
+<td style="text-align: center;">1000</td>
+</tr>
+</tbody>
+</table>
+
+
+
+Tusker:
+-------
+
+*last generated Wed Oct 24 14:47:57 2018*
+
+<table style="width:100%;">
+<colgroup>
+<col style="width: 8%" />
+<col style="width: 11%" />
+<col style="width: 18%" />
+<col style="width: 18%" />
+<col style="width: 19%" />
+<col style="width: 7%" />
+<col style="width: 7%" />
+<col style="width: 7%" />
+</colgroup>
+<thead>
+<tr class="header">
+<th>Partition</th>
+<th>Owner</th>
+<th>Node total (NODExCPU/MEM/FEATURE)</th>
+<th>Description</th>
+<th>SLURM Specification</th>
+<th style="text-align: center;">Max Job Run Time</th>
+<th style="text-align: center;">Max CPUs Per User</th>
+<th style="text-align: center;">Max Jobs Per User</th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td>batch</td>
+<td>shared</td>
+<td>38 total (38x64/256GB/none)</td>
+<td>(default, no specification)</td>
+<td>#SBATCH --partition=batch</td>
+<td style="text-align: center;">7-00:00:00</td>
+<td style="text-align: center;">2000</td>
+<td style="text-align: center;">1000</td>
+</tr>
+<tr class="even">
+<td>highmem</td>
+<td>shared</td>
+<td>4 total (2x64/1020GB/none; 2x64/512GB/none)</td>
+<td>Shared resources</td>
+<td>#SBATCH --partition=highmem</td>
+<td style="text-align: center;">7-00:00:00</td>
+<td style="text-align: center;">128</td>
+<td style="text-align: center;">1000</td>
+</tr>
+<tr class="odd">
+<td>guda</td>
+<td>unmc_cbsb unmc_gudalab</td>
+<td>1 total (1x64/256GB/none)</td>
+<td>Dedicated resources</td>
+<td>#SBATCH --partition=guda</td>
+<td style="text-align: center;">7-00:00:00</td>
+<td style="text-align: center;">64</td>
+<td style="text-align: center;">1000</td>
+</tr>
+<tr class="even">
+<td>reid</td>
+<td>reid</td>
+<td>1 total (1x64/256GB/none)</td>
+<td>Dedicated resources</td>
+<td>#SBATCH --partition=reid</td>
+<td style="text-align: center;">7-00:00:00</td>
+<td style="text-align: center;">64</td>
+<td style="text-align: center;">1000</td>
+</tr>
+</tbody>
+</table>
+
+Two nodes have 512GB of memory instead of 256GB (Max Request = 500GB),
+and two have 1024GB of memory (Max Request = 1000GB).
+
+Priority for short jobs
+-----------------------
+
+To run short jobs for testing and development work, a job can specify a
+different quality of service (QoS). The *short* QoS increases a jobs
+priority so it will run as soon as possible.
+
+| <span style="color: rgb(0,51,102);">SLURM Specification</span> |
+|----------------------------------------------------------------|
+| `#SBATCH --qos=short` |
+
+Limits per user for 'short' QoS
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-warning confluence-information-macro-icon"></span>
+
+- 6 hour job run time
+- 2 jobs of 16 CPUs or fewer
+- No more than 256 CPUs in use for *short* jobs from all users
+
+<span style="color: rgb(0,0,0);">Limitations of Jobs</span>
+-----------------------------------------------------------
+
+<span style="color: rgb(0,0,0);">Overall limitations of maximum job wall
+time. CPUs, etc. are set for all jobs with the default setting (when the
+"–qos=" section is omitted) and "short" jobs (described as above) on
+Tusker and Crane. The limitations are shown in the following
+form.</span>
+
+<span style="color: rgb(0,0,0);"> </span>
+
+<table>
+<thead>
+<tr class="header">
+<th><div class="tablesorter-header-inner">
+<span style="color: rgb(0,0,0);"> </span>
+</div></th>
+<th><div class="tablesorter-header-inner">
+<span style="color: rgb(0,0,0);">SLURM Specification</span>
+</div></th>
+<th><div class="tablesorter-header-inner">
+<span style="color: rgb(0,0,0);">Max Job Run Time</span>
+</div></th>
+<th><div class="tablesorter-header-inner">
+<span style="color: rgb(0,0,0);">Max CPUs per User</span>
+</div></th>
+<th><div class="tablesorter-header-inner">
+<span style="color: rgb(0,0,0);">Max Jobs per User</span>
+</div></th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td><span style="color: rgb(0,0,0);">Default</span></td>
+<td><span style="color: rgb(0,0,0);">Leave blank</span></td>
+<td><span style="color: rgb(0,0,0);">7 days</span></td>
+<td><span style="color: rgb(0,0,0);">2000</span></td>
+<td><span style="color: rgb(0,0,0);">1000</span></td>
+</tr>
+<tr class="even">
+<td><span style="color: rgb(0,0,0);">Short</span></td>
+<td><span style="color: rgb(0,0,0);"><code>#SBATCH --qos=short</code></span></td>
+<td><span style="color: rgb(0,0,0);">6 hours</span></td>
+<td><span style="color: rgb(0,0,0);">16</span></td>
+<td><span style="color: rgb(0,0,0);">2</span></td>
+</tr>
+</tbody>
+</table>
+
+<span style="color: rgb(0,0,0);"> </span>
+
+<span style="color: rgb(0,0,0);">Please also note that the memory and
+local hard drive limits are subject to the physical limitations of the
+nodes, described in the resources capabilities section of [<span
+style="color: rgb(0,0,0);">HCC
+Documentation</span>](https://hcc-docs.unl.edu/display/HCCDOC/HCC+Documentation) and
+the partition sections above.</span>
+
+Owned Partitions
+----------------
+
+Partitions marked as owned by a group means only specific groups are
+allowed to submit jobs to that partition. Groups are manually added to
+the list allowed to submit jobs to the partition. If you are unable to
+submit jobs to a partition, and you feel that you should be, please
+contact <a href="mailto:hcc-support@unl.edu" class="external-link">hcc-support@unl.edu</a>.
+
+Guest Partition
+---------------
+
+The `guest` partition can be used by users and groups that do not own
+dedicated resources on Crane. Jobs running in the `guest` partition
+will run on the owned resources with Intel OPA interconnect. The jobs
+are preempted when the resources are needed by the resource owners and
+are restarted on another node.
+
+tmp\_anvil Partition
+--------------------
+
+We have put 27 Anvil nodes which are not running Openstack in this
+partition. They have Intel Xeon E5-2650 v3 2.30GHz 2 CPU/20 cores and
+256GB memory per node. However, they don't have Infiniband or OPA
+interconnect. They are suitable for serial or single node parallel jobs.
+The nodes in this partition are subjected to be drained and move to our
+Openstack cloud when more cloud resources are needed without notice in
+advance.
+
+Use of Infiniband or OPA
+------------------------
+
+Crane nodes use either Infiniband or Intel Omni-Path interconnects in
+the batch partition. Most users don't need to worry about which one to
+choose. Jobs will automatically be scheduled for either of them by the
+scheduler. However, if the user wants to use one of the interconnects
+exclusively, the SLURM constraint keyword is available. Here are the
+examples:
+
+<table>
+<thead>
+<tr class="header">
+<th><span style="color: rgb(0,51,102);">SLURM Specification Omni-Path</span></th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td><p>#SBATCH --constraint=opa</p>
+<code></code></td>
+</tr>
+</tbody>
+</table>
+
+
+
+<table>
+<thead>
+<tr class="header">
+<th><span style="color: rgb(0,51,102);">SLURM Specification Infiniband</span></th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td><p>#SBATCH --constraint=ib</p>
+<code></code></td>
+</tr>
+</tbody>
+</table>
+
+Document generated by Confluence on Oct 24, 2018 14:47
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/submitting_jobs/available_partitions_on_sandhills.md b/content/guides/submitting_jobs/available_partitions_on_sandhills.md
new file mode 100644
index 00000000..87fae2cc
--- /dev/null
+++ b/content/guides/submitting_jobs/available_partitions_on_sandhills.md
@@ -0,0 +1,109 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Submitting Jobs](Submitting-Jobs_332222.html)
+
+<span id="title-text"> HCC-DOCS : Available Partitions on Sandhills </span>
+===========================================================================
+
+Created by <span class="author"> Confluence Admin</span>, last modified
+by <span class="editor"> Josh Samuelson</span> on Oct 19, 2017
+
+Partitions are used in Sandhills to enforce ownership and priority for
+owned resources. You can view the partitions with the command `sinfo`.
+
+*last generated Wed Oct 24 14:47:57 2018*
+
+<table style="width:100%;">
+<colgroup>
+<col style="width: 8%" />
+<col style="width: 11%" />
+<col style="width: 18%" />
+<col style="width: 18%" />
+<col style="width: 19%" />
+<col style="width: 7%" />
+<col style="width: 7%" />
+<col style="width: 7%" />
+</colgroup>
+<thead>
+<tr class="header">
+<th>Partition</th>
+<th>Owner</th>
+<th>Node total (NODExCPU/MEM/FEATURE)</th>
+<th>Description</th>
+<th>SLURM Specification</th>
+<th style="text-align: center;">Max Job Run Time</th>
+<th style="text-align: center;">Max CPUs Per User</th>
+<th style="text-align: center;">Max Jobs Per User</th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td>batch</td>
+<td>shared</td>
+<td>92 total (49x64/192GB/ib,2300Mhz; 41x32/128GB/ib,2000Mhz; 2x48/256GB/none)</td>
+<td>(default, no specification)</td>
+<td>#SBATCH --partition=batch</td>
+<td style="text-align: center;">10-00:00:00</td>
+<td style="text-align: center;">2000Mhz:1312 2300Mhz:3136</td>
+<td style="text-align: center;">1000</td>
+</tr>
+<tr class="even">
+<td>sabirianov</td>
+<td>sabirianov</td>
+<td>4 total (4x64/192GB/ib,2300Mhz)</td>
+<td>Dedicated resources with ib or 2300Mhz</td>
+<td>#SBATCH --partition=sabirianov</td>
+<td style="text-align: center;">10-00:00:00</td>
+<td style="text-align: center;">2300Mhz:256</td>
+<td style="text-align: center;">1000</td>
+</tr>
+</tbody>
+</table>
+
+Specific CPU Frequency Selection
+--------------------------------
+
+Sandhills is a hetereogenous cluster in terms of individual node
+resources, even when 'owned' by a research group and allocated to a
+specific partition with limited access. So that researchers can
+constrain their jobs' deployment to nodes with specific CPU frequencies,
+HCC has added a 'feature' on each node that can be used to filter as
+part of submission requests. Currently there are nodes with processors
+operating at 2300Mhz and 2000Mhz. In order to select only nodes of a
+specific frequency one must add '–contraint=2000Mhz' to the SLURM
+specification (for example). One can see partitions, node names,
+features, and allocation status by using a command such as 'sinfo -N -o
+"%P %f %t %N".
+
+<span style="color: rgb(0,0,0);">Limitations of Jobs</span>
+-----------------------------------------------------------
+
+<span style="color: rgb(0,0,0);">There are no special QoS settings for
+Sandhills currently. All jobs are subject to the maximum 10 day run time
+and 1000 jobs per user.</span>
+
+Guest Partition
+---------------
+
+The `guest` partition can be used by users and groups that do not own
+resources on Sandhills but still want to run parallel applications.
+ Jobs running in the `guest` partition will run on the owned resources
+with a high performance interconnect optimized for parallel
+applications. The jobs are preempted when the resources are needed by
+the resource owners and are restarted on another node.
+
+Owned Partitions
+----------------
+
+Partitions marked as owned by a group means only specific groups are
+allowed to submit jobs to that partition. Groups are manually added to
+the list allowed to submit jobs to the partition. If you are unable to
+submit jobs to a partition, and you feel that you should be, please
+contact <a href="mailto:hcc-support@unl.edu" class="external-link">hcc-support@unl.edu</a>.
+
+
+
+Document generated by Confluence on Oct 24, 2018 14:47
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/submitting_jobs/hcc_acknowledgment_credit.md b/content/guides/submitting_jobs/hcc_acknowledgment_credit.md
new file mode 100644
index 00000000..80e02848
--- /dev/null
+++ b/content/guides/submitting_jobs/hcc_acknowledgment_credit.md
@@ -0,0 +1,341 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Submitting Jobs](Submitting-Jobs_332222.html)
+
+<span id="title-text"> HCC-DOCS : HCC Acknowledgment Credit </span>
+===================================================================
+
+Created by <span class="author"> Josh Samuelson</span>, last modified on
+Sep 27, 2017
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-info confluence-information-macro-icon"></span>
+
+To submit an acknowledgement and receive the credit, please use the form
+here:
+<a href="https://hcc.unl.edu/acknowledgement-submission" class="external-link">https://hcc.unl.edu/acknowledgement-submission</a>
+
+### What is HCC Acknowledgment Credit?
+
+Whenever a group acknowledges using HCC resources as part of their
+research work (dissertation, thesis, grant, publication, presentation,
+etc), HCC will allocate a time-limited quota of CPU and memory resources
+to the group *in the shared portion of the machine* that can be used
+with jobs to gain scheduling priority in Slurm. A Job submitted with an
+acknowledgment credit qos will be placed at the top of the list of
+pending jobs to start. Since this is for the shared portion of the
+machine, it may not start immediately like a Priority Access (owned
+partition) job will. This will, however, likely shorten the start time
+of the job considerably, depending on job requirements.
+
+
+
+Different types of research activities are awarded different amounts of
+time.
+
+
+
+The following table lists research activities and awarded time:
+
+| Research activity | 1x CPU Time |
+|---------------------|-------------|
+| dissertation | 2 years |
+| funded grant | 2 years |
+| journal publication | 2 years |
+| master thesis | 2 years |
+| poster presentation | 1 year |
+| undergrad thesis | 1 year |
+| unfunded grant | 6 months |
+
+
+
+Time is awarded evenly for compute and memory resources at a ratio of
+1CPU to 4GB of memory. The QoS remains active until either resource is
+exhausted.
+
+
+
+Why this ratio?
+
+All nodes in the Crane batch partition can meet this CPU to memory
+ratio.
+
+
+
+Why have this ratio?
+
+In short: fairness. All programs require CPU and memory to complete the
+tasks they were written to perform. Dividing the memory amount by the
+number of CPUs in the node allows a CPU to memory equivalency to be
+used. Time is awarded evenly to CPU and memory at this ratio. If a
+high core count job is running with memory requirements less that 4GB,
+the job would starve any pending high memory job from considering the
+otherwise idle memory resources on the nodes running the high core count
+job. Similarly, a high memory job may use all the memory on a node but
+only use a single CPU. Using the ratio will result in fair accounting
+of CPU and memory resources awarded.
+
+
+
+Column description of the hcc-ac utility
+
+| hcc-ac header | Description |
+|----------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| Slurm qos | The qos name that must be provided with the Slurm '--qos=ac\_<name>' argument |
+| CPUx1 time | Time remaining for a single CPU |
+| MEMx4GB time | Time remaining for 4GB of memory |
+| per-CPU AvgMEM | The per-CPU average memory size available for the CPU time remaining in the qos. If CPU time is consumed faster than memory time, this value will increase. If memory time is consumed faster than CPU time, this value will decrease. |
+
+
+
+Example of how to use the awarded time for the 'demo' group.
+
+
+
+The awarded time is reduced down to 10 minutes to show consumption
+changes with differing job resource requirements:
+
+
+
+All times are in days-hours:minutes:seconds as used in Slurm's '--time='
+argument.
+
+
+
+**Default output**
+
+``` syntaxhighlighter-pre
+[demo01@login.hcc_cluster ~]$ hcc-ac
++-----------+--------------+--------------+----------------+
+| Slurm qos | CPUx1 time | MEMx4GB time | per-CPU AvgMEM |
++-----------+--------------+--------------+----------------+
+| ac_demo | 0-00:10:00 | 0-00:10:00 | 4.0GB |
++-----------+--------------+--------------+----------------+
+```
+
+Use the Slurm quality of service argument '--qos' to gain access to the
+awarded time with increased priority:
+
+
+
+**--qos=ac\_demo**
+
+``` syntaxhighlighter-pre
+[demo01@login.hcc_cluster ~]$ srun --qos=ac_demo --ntasks=1 --mem=8g --time=1:00 /bin/sleep 60
+```
+
+**\*\*job runs for 60 seconds\*\***
+
+**After 60 second job**
+
+``` syntaxhighlighter-pre
+[demo01@login.hcc_cluster ~]$ hcc-ac
++-----------+--------------+--------------+----------------+
+| Slurm qos | CPUx1 time | MEMx4GB time | per-CPU AvgMEM |
++-----------+--------------+--------------+----------------+
+| ac_demo | 0-00:09:00 | 0-00:08:00 | 3.556GB |
++-----------+--------------+--------------+----------------+
+```
+
+1 CPU minute and 2 4GB memory minutes were consumed by the prior srun
+job.
+
+
+
+1 CPU minute ie, (--ntasks=1 --time=1:00)
+
+2 4GB minutes ie, (--ntasks=1 --mem=8G --time=1:00 \~= 1 8GB minute \~=
+2 4GB minutes)
+
+
+
+The remaining per-CPU average memory can be found with the following
+equation:
+
+
+
+(memory time remaining) / (cpu time remaining) \* 4
+
+
+
+ie, 8 / 9 \* 4 == 3.556
+
+
+
+Multiplying the remaining cpu time against the per-CPU average memory
+will give the same value as multiplying the remaining memory time
+against 4GB:
+
+
+
+ie, 9 \* 3.556 \~= 8 \* 4
+
+
+
+**--ntasks=4**
+
+``` syntaxhighlighter-pre
+[demo01@login.hcc_cluster ~]$ srun --qos=ac_demo --ntasks=4 --mem-per-cpu=2G --time=1:00 /bin/sleep 60
+```
+
+**\*\*job runs for 60 seconds\*\***
+
+
+
+**After 60 second job**
+
+``` syntaxhighlighter-pre
+[demo01@login.hcc_cluster ~]$ hcc-ac
++-----------+--------------+--------------+----------------+
+| Slurm qos | CPUx1 time | MEMx4GB time | per-CPU AvgMEM |
++-----------+--------------+--------------+----------------+
+| ac_demo | 0-00:05:00 | 0-00:06:00 | 4.8GB |
++-----------+--------------+--------------+----------------+
+```
+
+
+
+4 CPU minutes and 2 4GB minutes were consumed by the prior srun job.
+
+
+
+4 CPU minutes (--ntasks=4 --time=1:00)
+
+2 4GB minutes (--ntasks=4 --mem-per-cpu=2G --time=1:00 \~= 1 8GB minute
+\~= 2 4GB minutes)
+
+
+
+6 / 5 \* 4 == 4.8
+
+
+
+**Insufficient time**
+
+``` syntaxhighlighter-pre
+[demo01@login.hcc_cluster ~]$ srun --qos=ac_demo --ntasks=5 --mem-per-cpu=5000M --time=1:00 /bin/sleep 60
+srun: error: Unable to allocate resources: Job violates accounting/QOS policy (job submit limit, user's size and/or time limits)
+```
+
+
+
+An example of a job requesting more resources than what remains
+available in the qos.
+
+
+
+**corrected memory requirement**
+
+``` syntaxhighlighter-pre
+[demo01@login.hcc_cluster ~]$ srun --qos=ac_demo --ntasks=5 --mem-per-cpu=4800M --time=1:00 /bin/sleep 60
+```
+
+**\*\*job runs for 60 seconds\*\***
+
+
+
+**exhausted qos**
+
+``` syntaxhighlighter-pre
+[demo01@login.hcc_cluster ~]$ hcc-ac
++-----------+--------------+--------------+----------------+
+| Slurm qos | CPUx1 time | MEMx4GB time | per-CPU AvgMEM |
++-----------+--------------+--------------+----------------+
+| ac_demo | exhausted | exhausted | 0.0GB |
++-----------+--------------+--------------+----------------+
+```
+
+All remaining time was used. Any further submissions to the qos will be
+**denied at submission time**.
+
+
+
+All of the above **srun** arguments work the same with **sbatch** within
+the submit file header.
+
+
+
+**submit file example**
+
+``` syntaxhighlighter-pre
+[demo01@login.hcc_cluster ~]$ cat submit_test.slurm
+#!/bin/bash
+#SBATCH --ntasks=4
+#SBATCH --qos=ac_demo
+#SBATCH --ntasks=5
+#SBATCH --mem-per-cpu=4800M
+#SBATCH --time=1:00
+
+/bin/sleep 60
+[demo01@login.hcc_cluster ~]$ sbatch ./submit_test.slurm
+```
+
+
+
+CPU and memory time in the qos are only consumed when jobs run against
+the qos. Therefore it is possible for more jobs to be submitted
+requesting the qos than could ever be run with it. Once the qos is
+exhausted all pending jobs attempting to use it will remain in pending
+state until more time is added to the qos or the job is modified to not
+consider the qos as a job requirement.
+
+
+
+HCC will run a script periodically (hourly) to scan for jobs pending in
+this state and modify them to utilize the cluster's default qos.
+
+
+
+Sizing what can fit in the qos's time limits using Slurm's '--test-only'
+argument.
+
+
+
+You can attempt different combinations of --nodes, --ntasks,
+--ntasks-per-node, --mem-per-cpu= and --mem utilizing the '--test-only'
+argument to size the job against what time remains in the qos.
+
+
+
+For example, with the same 10 minute limit:
+
+
+
+**--test-only job to see if it fits within qos time limits**
+
+``` syntaxhighlighter-pre
+[demo01@login.hcc_cluster ~]$ hcc-ac
++-----------+--------------+--------------+----------------+
+| Slurm qos | CPUx1 time | MEMx4GB time | per-CPU AvgMEM |
++-----------+--------------+--------------+----------------+
+| ac_demo | 0-00:10:00 | 0-00:10:00 | 4.0GB |
++-----------+--------------+--------------+----------------+
+
+[demo01@login.hcc_cluster ~]$ srun --test-only --qos=ac_demo --ntasks=6 --time=2:00 --mem-per-cpu=4G
+allocation failure: Job violates accounting/QOS policy (job submit limit, user's size and/or time limits)
+
+[demo01@login.hcc_cluster ~]$ srun --test-only --qos=ac_demo --ntasks=5 --time=2:00 --mem-per-cpu=4G
+srun: Job <number> to start at YYYY-MM-DDTHH:MM:SS using 5 processors on compute_node
+
+
+[demo01@login.hcc_cluster ~]$ srun --test-only --qos=ac_demo --ntasks=5 --time=2:00 --mem=40G
+allocation failure: Job violates accounting/QOS policy (job submit limit, user's size and/or time limits)
+
+[demo01@login.hcc_cluster ~]$ srun --test-only --qos=ac_demo --ntasks=5 --time=2:00 --mem=20G
+srun: Job <number> to start at YYYY-MM-DDTHH:MM:SS using 5 processors on compute_node
+
+
+[demo01@login.hcc_cluster ~]$ srun --test-only --qos=ac_demo --ntasks=3 --time=3:00 --mem-per-cpu=12G
+allocation failure: Job violates accounting/QOS policy (job submit limit, user's size and/or time limits)
+
+[demo01@login.hcc_cluster ~]$ srun --test-only --qos=ac_demo --ntasks=2 --time=3:00 --mem-per-cpu=12G
+allocation failure: Job violates accounting/QOS policy (job submit limit, user's size and/or time limits)
+
+[demo01@login.hcc_cluster ~]$ srun --test-only --qos=ac_demo --ntasks=1 --time=3:00 --mem-per-cpu=12G
+srun: Job <number> to start at YYYY-MM-DDTHH:MM:SS using 1 processors on compute_node
+```
+
+Document generated by Confluence on Oct 24, 2018 14:48
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/submitting_jobs/job_dependencies.md b/content/guides/submitting_jobs/job_dependencies.md
new file mode 100644
index 00000000..1a571c9e
--- /dev/null
+++ b/content/guides/submitting_jobs/job_dependencies.md
@@ -0,0 +1,181 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Submitting Jobs](Submitting-Jobs_332222.html)
+
+<span id="title-text"> HCC-DOCS : Job Dependencies </span>
+==========================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified by
+<span class="editor"> Derek Weitzel</span> on Nov 05, 2013
+
+The job dependency feature of SLURM is useful when you need to run
+multiple jobs in a particular order. A standard example of this is a
+workflow in which the output from one job is used as the input to the
+next. Rather than continually check to see if one job has ended and
+then manually submit the next, all the jobs in the workflow can be
+submitted at once. SLURM will then run them in the proper order based
+on the conditions supplied.
+
+Syntax
+------
+
+The basic syntax is to include the `-d `option with the `sbatch` command
+for a new submission to indicate it depends on another job. You must
+also supply the condition and job id upon which it depends. SLURM
+supports several possible conditions; see the `sbatch`
+<a href="http://slurm.schedmd.com/sbatch.html" class="external-link">man page</a>
+for all the options. The example here uses `after``ok`, which instructs
+SLURM to only run the submitted job after the dependency job has
+terminated without error (exit code 0).
+
+This example is usually referred to as a "diamond" workflow. There are
+4 jobs total; the jobs are labeled A through D. Job A runs first. Jobs
+B and C both depend on Job A completing before they can run. Job D then
+depends on Jobs B and C completing.
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/4849718/4980738.png" title="Simple Dependencies" alt="Simple Dependencies" class="confluence-embedded-image" width="300" height="300" /></span>
+
+The SLURM submit files for each step are below.
+
+**JobA.submit** <span class="collapse-source expand-control"
+style="display:none;"><span
+class="expand-control-icon icon"> </span><span
+class="expand-control-text">Expand source</span></span> <span
+class="collapse-spinner-wrapper"></span>
+
+``` syntaxhighlighter-pre
+#!/bin/sh
+#SBATCH --job-name=JobA
+#SBATCH --time=00:05:00
+#SBATCH --ntasks=1
+#SBATCH --output=JobA.stdout
+#SBATCH --error=JobA.stderr
+echo "I'm job A"
+echo "Sample job A output" > jobA.out
+sleep 120
+```
+
+**JobB.submit** <span class="collapse-source expand-control"
+style="display:none;"><span
+class="expand-control-icon icon"> </span><span
+class="expand-control-text">Expand source</span></span> <span
+class="collapse-spinner-wrapper"></span>
+
+``` syntaxhighlighter-pre
+#!/bin/sh
+#SBATCH --job-name=JobB
+#SBATCH --time=00:05:00
+#SBATCH --ntasks=1
+#SBATCH --output=JobB.stdout
+#SBATCH --error=JobB.stderr
+echo "I'm job B"
+echo "I'm using output from job A"
+cat jobA.out >> jobB.out
+echo "" >> jobB.out
+echo "Sample job B output" >> jobB.out
+sleep 120
+```
+
+**JobC.submit** <span class="collapse-source expand-control"
+style="display:none;"><span
+class="expand-control-icon icon"> </span><span
+class="expand-control-text">Expand source</span></span> <span
+class="collapse-spinner-wrapper"></span>
+
+``` syntaxhighlighter-pre
+#!/bin/sh
+#SBATCH --job-name=JobC
+#SBATCH --time=00:05:00
+#SBATCH --ntasks=1
+#SBATCH --output=JobC.stdout
+#SBATCH --error=JobC.stderr
+echo "I'm job C"
+echo "I'm using output from job A"
+cat jobA.out >> jobC.out
+echo "" >> jobC.out
+echo "Sample job C output" >> jobC.out
+sleep 120
+```
+
+**JobD.submit** <span class="collapse-source expand-control"
+style="display:none;"><span
+class="expand-control-icon icon"> </span><span
+class="expand-control-text">Expand source</span></span> <span
+class="collapse-spinner-wrapper"></span>
+
+``` syntaxhighlighter-pre
+#!/bin/sh
+#SBATCH --job-name=JobD
+#SBATCH --time=00:05:00
+#SBATCH --ntasks=1
+#SBATCH --output=JobD.stdout
+#SBATCH --error=JobD.stderr
+echo "I'm job D"
+echo "I'm using output from jobs B and C"
+cat jobB.out >> jobD.out
+echo "" >> jobD.out
+cat jobC.out >> jobD.out
+echo "" >> jobD.out
+echo "Sample job D output" >> jobD.out
+sleep 120
+```
+
+To start the workflow, submit Job A first:
+
+**Submit Job A**
+
+``` syntaxhighlighter-pre
+[demo01@login.tusker demo01]$ sbatch JobA.submit
+Submitted batch job 666898
+```
+
+Now submit jobs B and C, using the job id from Job A to indicate the
+dependency:
+
+**Submit Jobs B and C**
+
+``` syntaxhighlighter-pre
+[demo01@login.tusker demo01]$ sbatch -d afterok:666898 JobB.submit
+Submitted batch job 666899
+[demo01@login.tusker demo01]$ sbatch -d afterok:666898 JobC.submit
+Submitted batch job 666900
+```
+
+Finally, submit Job D as depending on both jobs B and C:
+
+**Submit Job D**
+
+``` syntaxhighlighter-pre
+[demo01@login.tusker demo01]$ sbatch -d afterok:666899:666900 JobD.submit
+Submitted batch job 666901
+```
+
+Running `squeue` will now show all four jobs. The output from `squeue`
+will also indicate that Jobs B, C, and D are in a pending state because
+of the dependency.
+
+**squeue output**
+
+``` syntaxhighlighter-pre
+[demo01@login.tusker demo01]$ squeue -u demo01
+ JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
+ 666899 batch JobB demo01 PD 0:00 1 (Dependency)
+ 666900 batch JobC demo01 PD 0:00 1 (Dependency)
+ 666901 batch JobD demo01 PD 0:00 1 (Dependency)
+ 666898 batch JobA demo01 R 0:52 1 c2409
+```
+
+As the each job completes successfully, SLURM will run the job(s) in the
+workflow as resources become available.
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[SimpleDependencies.png](attachments/4849718/4980738.png) (image/png)
+
+Document generated by Confluence on Oct 24, 2018 14:48
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/submitting_jobs/monitoring_jobs.md b/content/guides/submitting_jobs/monitoring_jobs.md
new file mode 100644
index 00000000..d1bcd0fc
--- /dev/null
+++ b/content/guides/submitting_jobs/monitoring_jobs.md
@@ -0,0 +1,148 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Submitting Jobs](Submitting-Jobs_332222.html)
+
+<span id="title-text"> HCC-DOCS : Monitoring Jobs </span>
+=========================================================
+
+Created by <span class="author"> Carrie Brown</span>, last modified by
+<span class="editor"> Natasha Pavlovikj</span> on Sep 19, 2018
+
+Careful examination of running times, memory usage and output files will
+allow you to ensure the job completed correctly and give you a good idea
+of what memory and time limits to request in the future.
+
+### Monitoring Completed Jobs:
+
+To see the runtime and memory usage of a job that has completed, use the
+sacct command:
+
+``` syntaxhighlighter-pre
+sacct
+```
+
+Lists all jobs by the current user and displays information such as
+JobID, JobName, State, and ExitCode.
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/21070052/21070053.png" class="confluence-embedded-image" height="150" /></span>
+
+
+
+Coupling this command with the --format flag will allow you to see more
+than the default information about a job. Fields to display should be
+listed as a comma separated list after the --format flag (without
+spaces). For example, to see the Elapsed time and Maximum used memory by
+a job, this command can be used:
+
+``` syntaxhighlighter-pre
+sacct --format JobID,JobName,Elapsed,MaxRSS
+```
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/21070052/21070054.png" class="confluence-embedded-image" height="150" /></span>
+
+Additional arguments and format field information can be found in
+<a href="https://slurm.schedmd.com/sacct.html" class="external-link">the SLURM documentation.</a>
+
+### Monitoring Running Jobs:
+
+There are two ways to monitor running jobs, the top command and
+monitoring the cgroup files. Top is helpful when monitoring
+multi-process jobs, whereas the cgroup files provide information on
+memory usage. Both of these tools require the use of an interactive job
+on the same node as the job to be monitored.
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-error confluence-information-macro-icon"></span>
+
+If the job to be monitored is using all available resources for a node,
+the user will not be able to obtain a simultaneous interactive job.
+
+After the job to be monitored is submitted and has begun to run, request
+an interactive job on the same node using the srun command:
+
+``` syntaxhighlighter-pre
+srun --jobid=<JOB_ID> --pty bash
+```
+
+Where <JOB\_ID> is replaced by the job id for the monitored job as
+assigned by SLURM.
+
+Alternately, you can request the interactive job by nodename as follows:
+
+``` syntaxhighlighter-pre
+srun --nodelist=<NODE_ID> --pty bash
+```
+
+Where <NODE\_ID> is replaced by the node name that the monitored
+job is running. This information can be found out by looking at the
+squeue output under the NODELIST column.
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/21070052/21070055.png" class="confluence-embedded-image" width="700" /></span>
+
+Once the interactive job begins, you can run top to view the processes
+on the node you are on:
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/21070052/21070056.png" class="confluence-embedded-image" height="400" /></span>
+
+Output for top displays each running process on the node. From the above
+image, we can see the various MATLAB processes being run by user
+cathrine98. To filter the list of processes, you can type \`u\` followed
+by the username of the user who owns the processes. To exit this screen,
+press \`q\`.
+
+During a running job, the cgroup folder is created which contains much
+of the information used by sacct. These files can provide a live
+overview of resources used for a running job. To access the cgroup
+files, you will need to be in an interactive job on the same node as the
+monitored job. To view specific files, and information, use one of the
+following commands:
+
+##### To view current memory usage:
+
+``` syntaxhighlighter-pre
+less /cgroup/memory/slurm/uid_<UID>/job_<SLURM_JOB_ID>/memory.usage_in_bytes
+```
+
+Where <UID> is replaced by your UID and <SLURM\_JOB\_ID> is
+replaced by the monitored job's Job ID as assigned by Slurm.
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-info confluence-information-macro-icon"></span>
+
+To find your uid, use the command \`id -u\`. Your UID never changes but
+is cluster specific (ie, your UID on Crane will always be the same but
+will differ from your UID on the other clusters).
+
+##### To view maximum memory usage from start of job to current point:
+
+``` syntaxhighlighter-pre
+cat /cgroup/memory/slurm/uid_${UID}/job_${SLURM_JOBID}/memory.max_usage_in_bytes
+```
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2017-7-10\_11-16-5.png](attachments/21070052/21070053.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2017-7-10\_11-16-36.png](attachments/21070052/21070054.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2017-7-10\_12-14-1.png](attachments/21070052/21070055.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2017-7-10\_12-23-27.png](attachments/21070052/21070056.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2017-7-10\_12-27-45.png](attachments/21070052/21070057.png)
+(image/png)
+
+Document generated by Confluence on Oct 24, 2018 14:48
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/submitting_jobs/submitting_a_job_array.md b/content/guides/submitting_jobs/submitting_a_job_array.md
new file mode 100644
index 00000000..e36ddf48
--- /dev/null
+++ b/content/guides/submitting_jobs/submitting_a_job_array.md
@@ -0,0 +1,56 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Submitting Jobs](Submitting-Jobs_332222.html)
+
+<span id="title-text"> HCC-DOCS : Submitting a Job Array </span>
+================================================================
+
+Created by <span class="author"> Derek Weitzel</span>, last modified by
+<span class="editor"> Carrie Brown</span> on Jun 29, 2017
+
+A job array is a set of jobs that share the same submit file, but will
+run multiple copies with a environment variable incremented. These are
+useful when you need to process a series of files, or if you need to run
+the same application multiple times.
+
+Creating a Array Submit File
+----------------------------
+
+An array submit file is very similar to the example submit files
+in [Submitting Jobs](Submitting-Jobs_332222.html).
+
+
+
+**example.slurm**
+
+``` syntaxhighlighter-pre
+#!/bin/sh
+#SBATCH --array=0-31
+#SBATCH --time=03:15:00 # Run time in hh:mm:ss
+#SBATCH --mem-per-cpu=1024 # Minimum memory required per CPU (in megabytes)
+#SBATCH --job-name=hello-world
+#SBATCH --error=/work/[groupname]/[username]/job.%A_%a.err
+#SBATCH --output=/work/[groupname]/[username]/job.%A_%a.out
+
+module load example/test
+
+echo "I am task $SLURM_ARRAY_TASK_ID on node `hostname`"
+sleep 60
+```
+
+The submit file above will output the `$SLURM_ARRAY_TASK_ID`, which will
+be different for every one of the 32 (0-31) jobs, to the output files.
+
+Job Arrays in SLURM have more features than this brief description,
+please visit
+the <a href="https://slurm.schedmd.com/job_array.html" class="external-link">SLURM Documentation</a> for
+more detailed information.
+
+
+
+
+
+Document generated by Confluence on Oct 24, 2018 14:47
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/submitting_jobs/submitting_an_interactive_job.md b/content/guides/submitting_jobs/submitting_an_interactive_job.md
new file mode 100644
index 00000000..2ede4ca6
--- /dev/null
+++ b/content/guides/submitting_jobs/submitting_an_interactive_job.md
@@ -0,0 +1,70 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Submitting Jobs](Submitting-Jobs_332222.html)
+
+<span id="title-text"> HCC-DOCS : Submitting an Interactive Job </span>
+=======================================================================
+
+Created by <span class="author"> Derek Weitzel</span>, last modified by
+<span class="editor"> Adam Caprez</span> on Sep 14, 2018
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-error confluence-information-macro-icon"></span>
+
+The `/home` directories are read-only on the worker nodes. You will need
+to compile or run your processing in `/work`.
+
+Submitting an interactive job is done with the command `srun`.
+
+``` syntaxhighlighter-pre
+$ srun --pty $SHELL
+```
+
+or to allocate 4 cores per node:
+
+``` syntaxhighlighter-pre
+$ srun --nodes=1 --ntasks-per-node=4 --mem-per-cpu=1024 --pty $SHELL
+```
+
+Submitting an interactive job is useful if you require extra resources
+to run some processing by hand. It is also very useful to debug your
+processing.
+
+And interactive job is scheduled onto a worker node just like a regular
+job. You can provide options to the interactive job just as you would a
+regular SLURM job.
+
+Priority for short jobs
+-----------------------
+
+To run short jobs for testing and development work, a job can specify a
+different quality of service (QoS). The *short* QoS increases a jobs
+priority so it will run as soon as possible.
+
+| <span style="color: rgb(0,51,102);">SLURM Specification</span> |
+|----------------------------------------------------------------|
+| `--qos=short` |
+
+Limits per user for 'short' QoS
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-warning confluence-information-macro-icon"></span>
+
+- 6 hour job run time
+- 2 jobs of 16 CPUs or fewer
+- No more than 256 CPUs in use for *short* jobs from all users
+
+**Using the short QoS**
+
+``` syntaxhighlighter-pre
+srun --qos=short --nodes=1 --ntasks-per-node=1 --mem-per-cpu=1024 --pty $SHELL
+```
+
+
+
+
+
+Document generated by Confluence on Oct 24, 2018 14:47
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/submitting_jobs/submitting_an_mpi_job.md b/content/guides/submitting_jobs/submitting_an_mpi_job.md
new file mode 100644
index 00000000..59f4aa5f
--- /dev/null
+++ b/content/guides/submitting_jobs/submitting_an_mpi_job.md
@@ -0,0 +1,1346 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Submitting Jobs](Submitting-Jobs_332222.html)
+
+<span id="title-text"> HCC-DOCS : Submitting an MPI Job </span>
+===============================================================
+
+Created by <span class="author"> Derek Weitzel</span>, last modified by
+<span class="editor"> Natasha Pavlovikj</span> on Sep 04, 2014
+
+This script requests 16 cores on nodes with InfiniBand:
+
+**mpi.submit**
+
+\#!/bin/sh
+\#SBATCH --ntasks=16
+\#SBATCH --mem-per-cpu=1024
+\#SBATCH --time=03:15:00
+\#SBATCH --error=/work/\[groupname\]/\[username\]/job.%J.err
+\#SBATCH --output=/work/\[groupname\]/\[username\]/job.%J.out
+
+
+
+| |
+|------------------------------------------|
+| module load compiler/gcc/8.2 openmpi/2.1 |
+
+mpirun /home/\[groupname\]/\[username\]/mpiprogram
+
+The above job will allocate 16 cores on the default partition. The 16
+cores could be on any of the nodes in the partition, even split between
+multiple nodes.
+
+Advanced Submission
+-------------------
+
+Some users may prefer to specify more details. This will allocate 32
+tasks, 16 on each of two nodes:
+
+**mpi.submit**
+
+\#!/bin/sh
+\#SBATCH --nodes=2
+\#SBATCH --ntasks-per-node=16
+\#SBATCH --mem-per-cpu=1024
+\#SBATCH --time=03:15:00
+\#SBATCH --error=/work/\[groupname\]/\[username\]/job.%J.err
+\#SBATCH --output=/work/\[groupname\]/\[username\]/job.%J.out
+
+
+
+| |
+|------------------------------------------|
+| module load compiler/gcc/8.2 openmpi/2.1 |
+
+mpirun /home/\[groupname\]/\[username\]/mpiprogram
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/332242/8127339.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/332242/8127409.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/332242/8127664.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[cb\_mpi.xsl](attachments/332242/8127418.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/332242/8127740.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/332242/8945694.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/332242/8945728.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/332242/8945787.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/332242/8945822.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/332242/8945856.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/332242/8945890.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/332242/8945942.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/332242/8946012.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/332242/9863198.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/332242/9863232.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/332242/9863284.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/332242/9863359.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/332242/9863415.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/332242/9863452.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/332242/9863551.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/332242/9863653.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/332242/9863710.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/332242/9863794.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/332242/9863846.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/332242/9863907.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/332242/10387508.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/332242/10944557.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/332242/35324891.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/332242/35325623.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/332242/35325736.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/332242/35326723.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/332242/8127220.xml)
+(application/octet-stream)
+
+Document generated by Confluence on Oct 24, 2018 14:47
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/submitting_jobs/submitting_an_openmp_job.md b/content/guides/submitting_jobs/submitting_an_openmp_job.md
new file mode 100644
index 00000000..0116a75d
--- /dev/null
+++ b/content/guides/submitting_jobs/submitting_an_openmp_job.md
@@ -0,0 +1,51 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Submitting Jobs](Submitting-Jobs_332222.html)
+
+<span id="title-text"> HCC-DOCS : Submitting an OpenMP Job </span>
+==================================================================
+
+Created by <span class="author"> Derek Weitzel</span>, last modified by
+<span class="editor"> Adam Caprez</span> on Jun 10, 2013
+
+Submitting an OpenMP job is different from [Submitting an MPI
+Job](Submitting-an-MPI-Job_332242.html) since you must request multiple
+cores from a single node.
+
+**OpenMP example submission**
+
+``` syntaxhighlighter-pre
+#!/bin/sh
+#SBATCH --ntasks-per-node=16 # 16 cores
+#SBATCH --nodes=1 # 1 node
+#SBATCH --mem-per-cpu=1024 # Minimum memory required per CPU (in megabytes)
+#SBATCH --time=03:15:00 # Run time in hh:mm:ss
+#SBATCH --error=/work/[groupname]/[username]/job.%J.err
+#SBATCH --output=/work/[groupname]/[username]/job.%J.out
+
+export OMP_NUM_THREADS=16
+./openmp-app.exe
+```
+
+Notice that we used `ntasks-per-node` to specify the number of cores we
+want on a single node. Additionally, we specify that we only want
+1 `node`.
+
+`OMP_NUM_THREADS` is required to limit the number of cores that OpenMP
+will use on the node. It should match the `ntasks-per-node` value.
+
+### Compiling
+
+Directions to compile OpenMP can be found on [Compiling an OpenMP
+Application](Compiling-an-OpenMP-Application_332316.html).
+
+### Further Documentation
+
+Further OpenMP documentation can be found on LLNL's
+<a href="https://computing.llnl.gov/tutorials/openMP/" class="external-link">OpenMP</a>
+website.
+
+Document generated by Confluence on Oct 24, 2018 14:47
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/submitting_jobs/submitting_cuda_or_openacc_jobs.md b/content/guides/submitting_jobs/submitting_cuda_or_openacc_jobs.md
new file mode 100644
index 00000000..fe0a993f
--- /dev/null
+++ b/content/guides/submitting_jobs/submitting_cuda_or_openacc_jobs.md
@@ -0,0 +1,1428 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Submitting Jobs](Submitting-Jobs_332222.html)
+
+<span id="title-text"> HCC-DOCS : Submitting CUDA or OpenACC Jobs </span>
+=========================================================================
+
+Created by <span class="author"> Derek Weitzel</span>, last modified by
+<span class="editor"> Zhongtao Zhang</span> on Mar 08, 2018
+
+GPUs available
+--------------
+
+Crane has four types of GPUs available in the **gpu** partition. The
+type of GPU is configured as a SLURM feature, so you can specify a type
+of GPU in your job resource requirements if necessary.
+
+<table>
+<thead>
+<tr class="header">
+<th>Description</th>
+<th>SLURM feature</th>
+<th>Available Hardware</th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td>Tesla K20, non-IB</td>
+<td>gpu_k20</td>
+<td>3 nodes - 2 GPUs per node</td>
+</tr>
+<tr class="even">
+<td>Tesla K20, with IB</td>
+<td>gpu_k20</td>
+<td>3 nodes - 3 GPUs per node</td>
+</tr>
+<tr class="odd">
+<td>Tesla K40, with IB</td>
+<td>gpu_k40</td>
+<td><p>5 nodes - 4 K40M GPUs per node</p>
+<p>1 node - 2 K40C GPUs per node</p></td>
+</tr>
+<tr class="even">
+<td>Tesla P100, with OPA</td>
+<td>gpu_p100</td>
+<td>2 nodes - 2 GPUs per node</td>
+</tr>
+</tbody>
+</table>
+
+To run your job on the next available GPU regardless of type, add the
+following options to your srun or sbatch command:
+
+``` syntaxhighlighter-pre
+--partition=gpu --gres=gpu
+```
+
+To run on a specific type of GPU, you can constrain your job to require
+a feature. To run on K40 GPUs for example:
+
+``` syntaxhighlighter-pre
+--partition=gpu --gres=gpu --constraint=gpu_k40
+```
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-warning confluence-information-macro-icon"></span>
+
+You may request multiple GPUs by changing the` --gres` value to
+-`-gres=gpu:2`. Note that this value is **per node**. For example,
+`--nodes=2 --gres=gpu:2 `will request 2 nodes with 2 GPUs each, for a
+total of 4 GPUs.
+
+Compiling
+---------
+
+Compilation of CUDA or OpenACC jobs must be performed on the GPU nodes.
+Therefore, you must run an [interactive
+job](Submitting-an-Interactive-Job_332265.html) to compile. An example
+command to compile in the **gpu** partition could be:
+
+``` syntaxhighlighter-pre
+$ srun --partition=gpu --gres=gpu --mem-per-cpu=1024 --ntasks-per-node=6 --nodes=1 --pty $SHELL
+```
+
+The above command will start a shell on a GPU node with 6 cores and 6GB
+of ram in order to compile a GPU job. The above command could also be
+useful if you want to run a test GPU job interactively.
+
+Submitting Jobs
+---------------
+
+CUDA and OpenACC submissions require running on GPU nodes.
+
+**cuda.submit**
+
+\#!/bin/sh
+\#SBATCH --time=03:15:00
+\#SBATCH --mem-per-cpu=1024
+\#SBATCH --job-name=cuda
+\#SBATCH --partition=gpu
+\#SBATCH --gres=gpu
+\#SBATCH --error=/work/\[groupname\]/\[username\]/job.%J.err
+\#SBATCH --output=/work/\[groupname\]/\[username\]/job.%J.out
+
+
+
+| |
+|----------------------|
+| module load cuda/6.5 |
+
+./cuda-app.exe
+
+
+
+OpenACC submissions require loading the PGI compiler (which is currently
+required to compile as well).
+
+**openacc.submit**
+
+\#!/bin/sh
+\#SBATCH --time=03:15:00
+\#SBATCH --mem-per-cpu=1024
+\#SBATCH --job-name=cuda-acc
+\#SBATCH --partition=gpu
+\#SBATCH --gres=gpu
+\#SBATCH --error=/work/\[groupname\]/\[username\]/job.%J.err
+\#SBATCH --output=/work/\[groupname\]/\[username\]/job.%J.out
+
+
+
+| |
+|--------------------------------------|
+| module load cuda/6.5 compiler/pgi/16 |
+
+./acc-app.exe
+
+Attachments:
+------------
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+
+Document generated by Confluence on Oct 24, 2018 14:48
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/submitting_jobs/submitting_htcondor_jobs.md b/content/guides/submitting_jobs/submitting_htcondor_jobs.md
new file mode 100644
index 00000000..04731eac
--- /dev/null
+++ b/content/guides/submitting_jobs/submitting_htcondor_jobs.md
@@ -0,0 +1,57 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Submitting Jobs](Submitting-Jobs_332222.html)
+
+<span id="title-text"> HCC-DOCS : Submitting HTCondor jobs </span>
+==================================================================
+
+Created by <span class="author"> Derek Weitzel</span>, last modified on
+Sep 13, 2013
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-warning confluence-information-macro-icon"></span>
+
+HTCondor is only available on Sandhills.
+
+If you require features of HTCondor, such as DAGMan or Pegasus,
+<a href="http://research.cs.wisc.edu/htcondor/" class="external-link">HTCondor</a> can
+submit jobs onto Sandhills using HTCondor's PBS integration. This can
+be done by adding `grid_resource = pbs` to the submit file. An example
+submission script is below:
+
+**submit.condor**
+
+``` syntaxhighlighter-pre
+universe = grid
+grid_resource = pbs
+executable = test.sh
+output = stuff.out
+error = stuff.err
+log = stuff.log
+batch_queue = guest
+queue
+```
+
+The above script will translate the condor submit file into a SLURM
+submit file, and execute the `test.sh` executable on a worker node.
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-error confluence-information-macro-icon"></span>
+
+The `/home` directories are read only on the Sandhills worker nodes. You
+have to submit your jobs from the `/work` directory just as you would in
+SLURM.
+
+Using Pegasus
+-------------
+
+If you are using
+<a href="http://pegasus.isi.edu/" class="external-link">Pegasus</a>,
+instructions on using the *glite* interface (as shown above) are
+available on the
+<a href="http://pegasus.isi.edu/wms/docs/latest/execution_environments.php#glite" class="external-link">User Guide</a>.
+
+Document generated by Confluence on Oct 24, 2018 14:48
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/submitting_jobs/submitting_jobs.md b/content/guides/submitting_jobs/submitting_jobs.md
new file mode 100644
index 00000000..d71a8bce
--- /dev/null
+++ b/content/guides/submitting_jobs/submitting_jobs.md
@@ -0,0 +1,229 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+
+<span id="title-text"> HCC-DOCS : Submitting Jobs </span>
+=========================================================
+
+Created by <span class="author"> Derek Weitzel</span>, last modified by
+<span class="editor"> Natasha Pavlovikj</span> on Aug 10, 2017
+
+Crane, Sandhills and Tusker are managed by
+the <a href="https://slurm.schedmd.com" class="external-link">SLURM</a> resource
+manager. In order to run processing on Crane, Sandhills or Tusker, you
+must create a SLURM script that will run your processing. After
+submitting the job, SLURM will schedule your processing on an available
+worker node.
+
+Before writing a submit file, you may need to [compile your
+application](Compiling-Source-Code_332258.html).
+
+- [Ensure proper working directory for job
+ output](#SubmittingJobs-Ensureproperworkingdirectoryforjoboutput)
+- [Creating a SLURM Submit
+ File](#SubmittingJobs-CreatingaSLURMSubmitFile)
+- [Submitting the job](#SubmittingJobs-Submittingthejob)
+- [Checking Job Status](#SubmittingJobs-CheckingJobStatus)
+ - [Checking Job Start](#SubmittingJobs-CheckingJobStart)
+- [Next Steps](#SubmittingJobs-NextSteps)
+
+Ensure proper working directory for job output
+----------------------------------------------
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-warning confluence-information-macro-icon"></span>
+
+All SLURM job output should be directed to your /work path.
+
+**manual specification of /work path**
+
+``` syntaxhighlighter-pre
+$ cd /work/[groupname]/[username]
+```
+
+The environment variable $WORK can also be used.
+
+**using environment for /work path**
+
+``` syntaxhighlighter-pre
+$ cd $WORK
+$ pwd
+/work/[groupname]/[username]
+```
+
+Review how /work differs from /home [here.](Handling-Data_332256.html)
+
+Creating a SLURM Submit File
+----------------------------
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-warning confluence-information-macro-icon"></span>
+
+The below example is for a serial job. For submitting MPI jobs, please
+look at the [MPI Submission Guide.](Submitting-an-MPI-Job_332242.html)
+
+A SLURM submit file is broken into 2 sections, the job description and
+the processing. SLURM job description are prepended with `#SBATCH` in
+the submit file.
+
+**SLURM Submit File**
+
+``` syntaxhighlighter-pre
+#!/bin/sh
+#SBATCH --time=03:15:00 # Run time in hh:mm:ss
+#SBATCH --mem-per-cpu=1024 # Maximum memory required per CPU (in megabytes)
+#SBATCH --job-name=hello-world
+#SBATCH --error=/work/[groupname]/[username]/job.%J.err
+#SBATCH --output=/work/[groupname]/[username]/job.%J.out
+
+module load example/test
+
+hostname
+sleep 60
+```
+
+- **time**
+ Maximum walltime the job can run. After this time has expired, the
+ job will be stopped.
+- **mem-per-cpu**
+ Memory that is allocated per core for the job. If you exceed this
+ memory limit, your job will be stopped.
+- **mem**
+ Specify the real memory required per node in MegaBytes. If you
+ exceed this limit, your job will be stopped. Note that for you
+ should ask for less memory than each node actually has. For
+ instance, Tusker has 1TB, 512GB and 256GB of RAM per node. You may
+ only request 1000GB of RAM for the 1TB node, 500GB of RAM for the
+ 512GB nodes, and 250GB of RAM for the 256GB nodes. For Crane, the
+ max is 500GB.
+- **job-name
+ **The name of the job. Will be reported in the job listing.
+- **partition**
+ The partition the job should run in. Partitions determine the job's
+ priority and on what nodes the partition can run on. See [Available
+ Partitions on
+ Sandhills](Available-Partitions-on-Sandhills_332211.html), and
+ [Available Partitions on Crane and
+ Tusker](https://hcc-docs.unl.edu/display/HCCDOC/Available+Partitions+on+Crane+and+Tusker) for
+ a list of possible partitions.
+- **error**
+ Location of the stderr will be written for the job. `[groupname]`
+ and `[username]` should be replaced your group name and username.
+ Your username can be retrieved with the command `id -un` and your
+ group with `id -ng`.
+- **output**
+ Location of the stdout will be written for the job.
+
+More advanced submit commands can be found on the
+<a href="https://slurm.schedmd.com/sbatch.html" class="external-link">SLURM Docs</a>.
+ You can also find an example of a MPI submission on [Submitting an MPI
+Job](Submitting-an-MPI-Job_332242.html).
+
+Submitting the job
+------------------
+
+Submitting the SLURM job is done by command `sbatch`. SLURM will read
+the submit file, and schedule the job according to the description in
+the submit file.
+
+Submitting the job described above is:
+
+**SLURM Submission**
+
+``` syntaxhighlighter-pre
+$ sbatch example.slurm
+Submitted batch job 24603
+```
+
+The job was successfully submitted.
+
+Checking Job Status
+-------------------
+
+Job status is found with the command `squeue`. It will provide
+information such as:
+
+- The State of the job:
+ - **R** - Running
+ - **PD** - Pending - <span style="color: rgb(0,0,0);">Job is
+ awaiting resource allocation.</span>
+ - <span style="color: rgb(0,0,0);">Additional codes are available
+ on the
+ <a href="http://slurm.schedmd.com/squeue.html" class="external-link">squeue</a>
+ page.</span><span style="color: rgb(0,0,0);">
+ </span>
+- <span style="color: rgb(0,0,0);">Job Name</span>
+- <span style="color: rgb(0,0,0);">Run Time</span>
+- <span style="color: rgb(0,0,0);">Nodes running the job</span>
+
+Checking the status of the job is easiest by filtering by your username,
+using the `-u` option to squeue.
+
+``` syntaxhighlighter-pre
+$ squeue -u <username>
+ JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
+ 24605 batch hello-wo <username> R 0:56 1 b01
+```
+
+Additionally, if you want to see the status of a specific partition, for
+example if you are part of a
+[partition](Available-Partitions-on-Sandhills_332211.html), you can use
+the `-p` option to `squeue`:
+
+``` syntaxhighlighter-pre
+$ squeue -p esquared
+ JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
+ 73435 esquared MyRandom tingting R 10:35:20 1 ri19n10
+ 73436 esquared MyRandom tingting R 10:35:20 1 ri19n12
+ 73735 esquared SW2_driv hroehr R 10:14:11 1 ri20n07
+ 73736 esquared SW2_driv hroehr R 10:14:11 1 ri20n07
+```
+
+### Checking Job Start
+
+You may view the start time of your job with the
+command `squeue --start`. The output of the command will show the
+expected start time of the jobs.
+
+``` syntaxhighlighter-pre
+$ squeue --start --user lypeng
+ JOBID PARTITION NAME USER ST START_TIME NODES NODELIST(REASON)
+ 5822 batch Starace lypeng PD 2013-06-08T00:05:09 3 (Priority)
+ 5823 batch Starace lypeng PD 2013-06-08T00:07:39 3 (Priority)
+ 5824 batch Starace lypeng PD 2013-06-08T00:09:09 3 (Priority)
+ 5825 batch Starace lypeng PD 2013-06-08T00:12:09 3 (Priority)
+ 5826 batch Starace lypeng PD 2013-06-08T00:12:39 3 (Priority)
+ 5827 batch Starace lypeng PD 2013-06-08T00:12:39 3 (Priority)
+ 5828 batch Starace lypeng PD 2013-06-08T00:12:39 3 (Priority)
+ 5829 batch Starace lypeng PD 2013-06-08T00:13:09 3 (Priority)
+ 5830 batch Starace lypeng PD 2013-06-08T00:13:09 3 (Priority)
+ 5831 batch Starace lypeng PD 2013-06-08T00:14:09 3 (Priority)
+ 5832 batch Starace lypeng PD N/A 3 (Priority)
+```
+
+The output shows the expected start time of the jobs, as well as the
+reason that the jobs are currently idle (in this case, low priority of
+the user due to running numerous jobs already).
+
+
+
+<span
+style="color: rgb(0,0,0);font-size: 20.0px;line-height: 1.5;">Removing
+the Job</span>
+
+Removing the job is done with the `scancel` command. The only argument
+to the `scancel` command is the job id. For the job above, the command
+is:
+
+``` syntaxhighlighter-pre
+$ scancel 24605
+```
+
+Next Steps
+----------
+
+
+
+Document generated by Confluence on Oct 24, 2018 14:47
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/submitting_jobs/submitting_matlab_jobs.md b/content/guides/submitting_jobs/submitting_matlab_jobs.md
new file mode 100644
index 00000000..be98af34
--- /dev/null
+++ b/content/guides/submitting_jobs/submitting_matlab_jobs.md
@@ -0,0 +1,1360 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Submitting Jobs](Submitting-Jobs_332222.html)
+
+<span id="title-text"> HCC-DOCS : Submitting Matlab Jobs </span>
+================================================================
+
+Created by <span class="author"> Derek Weitzel</span>, last modified by
+<span class="editor"> Jingchao Zhang</span> on Mar 30, 2018
+
+Submitting Matlab jobs is very similar to [submitting MPI
+jobs](Submitting-an-MPI-Job_332242.html) or [serial
+jobs](Submitting-Jobs_332222.html) (depending if you are using parallel
+matlab).
+
+Submit File
+-----------
+
+The submit file will need to be modified to allow Matlab to work.
+ Specifically, these two lines should be added before calling matlab:
+
+**serial\_matlab.submit**
+
+\#!/bin/sh
+\#SBATCH --time=03:15:00
+\#SBATCH --mem-per-cpu=1024
+\#SBATCH --job-name=\[job\_name\]
+\#SBATCH --error=/work/\[groupname\]/\[username\]/job.%J.err
+\#SBATCH --output=/work/\[groupname\]/\[username\]/job.%J.out
+
+module load matlab/r2014b
+
+matlab -nodisplay -r "\[matlab script name\], quit"
+
+
+
+<span style="color: rgb(0,0,0);">Parallel Matlab .m file</span>
+---------------------------------------------------------------
+
+The submit file:
+
+**parallel\_matlab.submit**
+
+\#!/bin/sh
+\#SBATCH --nodes=1
+\#SBATCH --ntasks-per-node=5
+\#SBATCH --time=03:15:00
+\#SBATCH --mem-per-cpu=1024
+\#SBATCH --job-name=\[job\_name\]
+\#SBATCH --error=/work/\[groupname\]/\[username\]/job.%J.err
+\#SBATCH --output=/work/\[groupname\]/\[username\]/job.%J.out
+
+module load matlab/r2014b
+
+matlab -nodisplay -r "\[matlab script name\], quit"
+
+
+
+In addition to the changes in the submit file, if you are running
+parallel Matlab, you will also need to add to the .m file an additional
+line.
+
+**Matlab File Additions**
+
+``` syntaxhighlighter-pre
+...
+i=str2num(getenv('SLURM_TASKS_PER_NODE'));
+parpool(i);
+...
+```
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/2097230/8127341.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/2097230/8127411.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/2097230/8127666.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[cb\_matlab.xsl](attachments/2097230/8127421.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/2097230/8127742.xml)
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/2097230/8946014.xml)
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/2097230/9863200.xml)
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/2097230/9863286.xml)
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+[tusker\_modules.xml](attachments/2097230/9863848.xml)
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+[tusker\_modules.xml](attachments/2097230/11633554.xml)
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+[tusker\_modules.xml](attachments/2097230/11633639.xml)
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+[tusker\_modules.xml](attachments/2097230/11633680.xml)
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+[tusker\_modules.xml](attachments/2097230/35324603.xml)
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+[tusker\_modules.xml](attachments/2097230/35324893.xml)
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/2097230/35325625.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/2097230/35325738.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/2097230/35326725.xml)
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+[tusker\_modules.xml](attachments/2097230/8127234.xml)
+(application/octet-stream)
+
+Document generated by Confluence on Oct 24, 2018 14:48
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/guides/submitting_jobs/submitting_r_jobs.md b/content/guides/submitting_jobs/submitting_r_jobs.md
new file mode 100644
index 00000000..8ae91505
--- /dev/null
+++ b/content/guides/submitting_jobs/submitting_r_jobs.md
@@ -0,0 +1,1611 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Submitting Jobs](Submitting-Jobs_332222.html)
+
+<span id="title-text"> HCC-DOCS : Submitting R jobs </span>
+===========================================================
+
+Created by <span class="author"> Derek Weitzel</span>, last modified by
+<span class="editor"> Natasha Pavlovikj</span> on Apr 04, 2018
+
+<span
+style="color: rgb(51,51,51);font-size: 14.0px;line-height: 1.4285715;">Submitting
+an R job is very similar to submitting a serial job shown
+on </span>[Submitting Jobs](Submitting-Jobs_332222.html)
+
+<span
+style="color: rgb(51,51,51);font-size: 14.0px;line-height: 1.4285715;"></span>
+
+- [Running R scripts in
+ batch](#SubmittingRjobs-RunningRscriptsinbatch)
+ - [Running R scripts using \`R CMD
+ BATCH\`](#SubmittingRjobs-RunningRscriptsusing%60RCMDBATCH%60)
+ - [Running R scripts using
+ \`Rscript\`](#SubmittingRjobs-RunningRscriptsusing%60Rscript%60)
+- [Multicore (parallel) R
+ submission](#SubmittingRjobs-Multicore(parallel)Rsubmission)
+- [Multinode R submission with
+ Rmpi](#SubmittingRjobs-MultinodeRsubmissionwithRmpi)
+- [Adding packages](#SubmittingRjobs-Addingpackages)
+ - [Installing packages
+ interactively](#SubmittingRjobs-Installingpackagesinteractively)
+ - [Installing packages using R CMD
+ INSTALL](#SubmittingRjobs-InstallingpackagesusingRCMDINSTALL)
+
+
+
+Running R scripts in batch
+--------------------------
+
+<span
+style="color: rgb(51,51,51);font-size: 14.0px;line-height: 1.4285715;">There
+are two primary commands to use when submitting R scripts: \`Rscript\`
+and \`R CMD BATCH\`. Both commands will execute the passed script but
+differ in the way they process output.</span>
+
+#### <span style="color: rgb(51,51,51);font-size: 14.0px;line-height: 1.4285715;">Running R scripts using \`R CMD BATCH\` </span>
+
+<span
+style="color: rgb(51,51,51);font-size: 14.0px;line-height: 1.4285715;">When
+utilizing \`R CMD BATCH\` all output will be directed to an \`.Rout\`
+file named after your script unless otherwise specified. For
+example:</span>
+
+**serial\_R.submit**
+
+\#!/bin/sh
+\#SBATCH --time=00:30:00
+\#SBATCH --mem-per-cpu=1024
+\#SBATCH --job-name=TestJob
+
+
+
+| |
+|-------------------|
+| module load R/3.3 |
+
+R CMD BATCH Rcode.R
+
+<span
+style="color: rgb(51,51,51);font-size: 14.0px;line-height: 1.4285715;">In
+the above example, output for the job will be found in the file
+\`Rcode.Rout\`. Notice that we did not specify output and error files in
+our SLURM directives, these are not needed as all R output will go into
+the \`.Rout\` file. To direct output to a specific location, follow your
+\`R CMD BATCH\` command with the name of the file where you want output
+directed to, as follows:</span>
+
+
+
+**serial\_R.submit**
+
+\#!/bin/sh
+\#SBATCH --time=00:30:00
+\#SBATCH --mem-per-cpu=1024
+\#SBATCH --job-name=TestJob
+
+
+
+| |
+|-------------------|
+| module load R/3.3 |
+
+R CMD BATCH Rcode.R Rcodeoutput.txt
+
+<span
+style="color: rgb(51,51,51);font-size: 14.0px;line-height: 1.4285715;">In
+this example, output from running the script \`Rcode.R\` will be placed
+in the file \`Rcodeoutput.txt\`.
+</span>
+
+To pass arguments to the script, they need to be specified after \`R CMD
+BATCH\` but before the script to be executed, and preferably preceded
+with \`--args\` as follows:
+
+**serial\_R.submit**
+
+\#!/bin/sh
+\#SBATCH --time=00:30:00
+\#SBATCH --mem-per-cpu=1024
+\#SBATCH --job-name=TestJob
+
+
+
+| |
+|-------------------|
+| module load R/3.3 |
+
+R CMD BATCH "–args argument1 argument2 argument3" Rcode.R
+Rcodeoutput.txt
+
+#### Running R scripts using \`Rscript\`
+
+Using \`Rscript\` to execute R scripts differs from R CMD BATCH in that
+all output and errors from the script are directed to STDOUT and STDERR
+in a manner similar to other programs. This gives the user larger
+control over where to direct the output. For example, to run our script
+using \`Rscript\` the submit script could look like the following:
+
+**serial\_R.submit**
+
+\#!/bin/sh
+\#SBATCH --time=00:30:00
+\#SBATCH --mem-per-cpu=1024
+\#SBATCH --job-name=TestJob
+\#SBATCH --error=TestJob.%J.stderr
+\#SBATCH --output=TestJob.%J.stdout
+
+
+
+| |
+|-------------------|
+| module load R/3.3 |
+
+Rscript Rcode.R
+
+In the above example, STDOUT will be directed to the output file
+\`TestJob.%J.stdout\` and STDERR directed to \`TestJob.%J.stderr\`. You
+will notice that the example is very similar to to the [serial
+example](Submitting-Jobs_332222.html). The important line is the
+`module load` command. That tells Tusker to load the R framework into
+the environment so jobs may use it.
+
+To pass arguments to the script when using \`Rscript\`, the arguments
+will follow the script name as in the example below:
+
+**serial\_R.submit**
+
+\#!/bin/sh
+\#SBATCH --time=00:30:00
+\#SBATCH --mem-per-cpu=1024
+\#SBATCH --job-name=TestJob
+\#SBATCH --error=TestJob.%J.stderr
+\#SBATCH --output=TestJob.%J.stdout
+
+
+
+| |
+|-------------------|
+| module load R/3.3 |
+
+Rscript Rcode.R argument1 argument2 argument3
+
+Multicore (parallel) R submission
+---------------------------------
+
+Submitting a multicore R job to SLURM is very similar to [Submitting an
+OpenMP Job](Submitting-an-OpenMP-Job_332306.html), since both are
+running multicore jobs on a single node. Below is an example:
+
+**parallel\_R.submit**
+
+\#!/bin/sh
+\#SBATCH --ntasks-per-node=16
+\#SBATCH --nodes=1
+\#SBATCH --time=00:30:00
+\#SBATCH --mem-per-cpu=1024
+\#SBATCH --job-name=TestJob
+\#SBATCH --error=TestJob.%J.stdout
+\#SBATCH --output=TestJob.%J.stderr
+
+
+
+| |
+|-------------------|
+| module load R/3.3 |
+
+R CMD BATCH Rcode.R
+
+The above example will submit a single job which can use up to 16 cores.
+
+
+Be sure to use limits in your R code so you only use 16 cores, or your
+performance will suffer. For example, when using the
+<a href="http://stat.ethz.ch/R-manual/R-devel/library/parallel/doc/parallel.pdf" class="external-link">parallel</a>
+package function mclapply:
+
+**parallel.R**
+
+``` syntaxhighlighter-pre
+library("parallel")
+...
+mclapply(rep(4, 5), rnorm, mc.cores=16)
+```
+
+Multinode R submission with Rmpi
+--------------------------------
+
+Submitting a multinode MPI R job to SLURM is very similar to [Submitting
+an MPI Job](Submitting-an-MPI-Job_332242.html), since both are running
+multicore jobs on a multiple nodes. Below is an example of running Rmpi
+on Crane on 2 nodes and 32 cores:
+
+**Rmpi.submit**
+
+\#!/bin/sh
+\#SBATCH --nodes=2
+\#SBATCH --ntasks-per-node=16
+\#SBATCH --time=00:30:00
+\#SBATCH --mem-per-cpu=1024
+\#SBATCH --job-name=TestJob
+\#SBATCH --error=TestJob.%J.stdout
+\#SBATCH --output=TestJob.%J.stderr
+
+module load compiler/gcc/4.9 openmpi/1.10 R/3.3
+export OMPI\_MCA\_mtl=^psm
+mpirun -n 1 R CMD BATCH Rmpi.R
+
+When you run Rmpi job on Crane, please use the line **export
+OMPI\_MCA\_mtl=^psm** in your submit script. On the other hand, if you
+run Rmpi job on Tusker, you **do not need** to add this line. This is
+because of the different Infiniband cards Tusker and Crane use.
+Regardless of how may cores your job uses, the Rmpi package should
+always be run with **mpirun -n 1** because it spawns additional
+processes dynamically.
+
+Please find below an example of Rmpi R script provided by
+<a href="https://rcc.uchicago.edu/docs/software/environments/R/index.html#rmpi" class="external-link">The University of Chicago Research Computing Center</a>:
+
+**Rmpi.R**
+
+``` syntaxhighlighter-pre
+library(Rmpi)
+
+# initialize an Rmpi environment
+ns <- mpi.universe.size()
+mpi.spawn.Rslaves(nslaves=ns)
+
+# send these commands to the slaves
+mpi.bcast.cmd( id <- mpi.comm.rank() )
+mpi.bcast.cmd( ns <- mpi.comm.size() )
+mpi.bcast.cmd( host <- mpi.get.processor.name() )
+
+# all slaves execute this command
+mpi.remote.exec(paste("I am", id, "of", ns, "running on", host))
+
+# close down the Rmpi environment
+mpi.close.Rslaves(dellog = FALSE)
+mpi.exit()
+```
+
+Adding packages
+---------------
+
+There are two options to install packages. The first is to run R on the
+login node and run R interactively to install packages. The second is to
+use the \`R CMD INSTALL\` command.
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-info confluence-information-macro-icon"></span>
+
+All R packages must be installed from the login node. R libraries are
+stored in user's home directories which are not writable from the worker
+nodes.
+
+#### Installing packages interactively
+
+1. Load the R module with the command \`module load R\`
+ 1. Note that each version of R uses its own user libraries. To
+ install packages under a specific version of R, specify which
+ version by using the module load command followed by the version
+ number. For example, to load R version 3.3, you would use the
+ command \`module load R/3.3\`
+2. Run R interactively using the command \`R\`
+3. From within R, use the \`install.packages()\` command to install
+ desired packages. For example, to install the package \`ggplot2\`
+ use the command \`install.packages("ggplot2")
+
+Some R packages, require external compilers or additional libraries. If
+you see an error when installing your package you might need to load
+additional modules to make these compilers or libraries available. For
+more information about this, refer to the package documentation.
+
+#### Installing packages using R CMD INSTALL
+
+To install packages using \`R CMD INSTALL\` the zipped package must
+already be downloaded to the cluster. You can download package source
+using \`wget\`. Then the \`R CMD INSTALL\` command can be used when
+pointed to the full path of the source tar file. For example, to install
+ggplot2 the following commands are used:
+
+``` syntaxhighlighter-pre
+# Download the package source:
+wget https://cran.r-project.org/src/contrib/ggplot2_2.2.1.tar.gz
+
+# Install the package:
+R CMD INSTALL ./ggplot2_2.2.1.tar.gz
+```
+
+Additional information on using the \`R CMD INSTALL\` command can be
+found in the R documentation which can be seen by typing \`?INSTALL\`
+within the R console.
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/2098144/8127342.xml)
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/2098144/35325741.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/2098144/35326728.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/2098144/8127243.xml)
+(application/octet-stream)
+
+Document generated by Confluence on Oct 24, 2018 14:48
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/quickstarts/_index.md b/content/quickstarts/_index.md
new file mode 100644
index 00000000..d2f1201d
--- /dev/null
+++ b/content/quickstarts/_index.md
@@ -0,0 +1,10 @@
++++
+title = "Quickstarts"
+weight = "10"
++++
+
+The quick start guides require that you already have a HCC account. You
+can get a HCC account by applying on the
+[HCC website] (http://hcc.unl.edu/newusers/)
+
+{{% children %}}
diff --git a/content/quickstarts/bash_commands.md b/content/quickstarts/bash_commands.md
new file mode 100644
index 00000000..a7a1837e
--- /dev/null
+++ b/content/quickstarts/bash_commands.md
@@ -0,0 +1,217 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Quick Start Guides](Quick-Start-Guides_1245279.html)
+
+<span id="title-text"> HCC-DOCS : Bash Commands </span>
+=======================================================
+
+Created by <span class="author"> Carrie Brown</span>, last modified on
+Oct 26, 2017
+
+[Video Tutorial](#BashCommands-video)
+
+Holland clusters all run on the Linux operating system, similarly to how
+your personal computer might run Windows or Mac OS. However, unlike
+Windows or Mac OS, our systems do not utilize a graphical user interface
+where you can use a mouse to navigate and initiate commands. Instead, we
+use a command line interface, where the user types in commands which are
+then processed and text output is displayed on the screen. The default
+shell used is Bash. Bash may seem complicated to learn at first, but
+with just a small handful of commands, you can do anything that you
+would usually do with a mouse. **In fact, once people become proficient
+in Bash, many of them prefer it over graphical interfaces due to its
+versatility and performance.**
+
+Below, we have compiled a list of common commands and usage examples.
+For a more information, check out one of these references:
+
+- <a href="https://eharstad.github.io/shell-novice/" class="external-link">Software Carpentry's "Introduction to the Bash Shell" Lesson</a> -
+ a great walkthrough of the basics of Bash designed for novice users
+- <a href="http://www.comptechdoc.org/os/linux/usersguide/" class="external-link">Linux Users Guide</a> -
+ detailed information about the Linux command line and how to utilize
+ it
+- <a href="https://www.cheatography.com/davechild/cheat-sheets/linux-command-line/" class="external-link">Linux Command Line Cheat Sheet</a> -
+ a quick reference for Linux commands. Offers a PDF version that you
+ can print out.
+
+Linux Commands Reference List:
+------------------------------
+
+<table>
+<tbody>
+<tr class="odd">
+<td>ls</td>
+<td>list: Lists the files and directories located in the current directory</td>
+<td><ul>
+<li>ls</li>
+<li>ls -a
+<ul>
+<li>shows all the files in the directory, including hidden ones</li>
+</ul></li>
+<li>ls -l
+<ul>
+<li>shows contents in a list format including information such as file size, file permissions and date the file was modified</li>
+</ul></li>
+<li>ls *.txt
+<ul>
+<li>shows all files in the current directory which end with .txt</li>
+</ul></li>
+</ul></td>
+</tr>
+<tr class="even">
+<td>cd</td>
+<td>change directory: this allows users to navigate in or out of file directories</td>
+<td><ul>
+<li>cd <folder path></li>
+<li>cd folder_name
+<ul>
+<li>navigates into directory "folder_name" located in the current directory</li>
+</ul></li>
+<li>cd ..
+<ul>
+<li>navigates out of a directory and into the parent directory</li>
+</ul>
+cd $HOME (or $WORK)
+<ul>
+<li>navigates to a user's home (or work) directory</li>
+</ul></li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td>mv</td>
+<td>move: used to move a file or directory to another location</td>
+<td><ul>
+<li>mv <current file(s)> <target file(s)></li>
+<li>mv * ../
+<ul>
+<li>moves all files from the current directory into the parent directory</li>
+</ul></li>
+<li>mv old_filename new_filename
+<ul>
+<li>renames the file "old_filename" to "new_filename"</li>
+</ul></li>
+</ul></td>
+</tr>
+<tr class="even">
+<td>cp</td>
+<td>copy: used to copy a file or directory to another location</td>
+<td><ul>
+<li>cp <current file(s)> <target file(s)></li>
+<li>cp * ../
+<ul>
+<li>copies all files in the current directory and puts the copies into the parent directory</li>
+</ul></li>
+<li>cp -r ./orig_folder ./new_folder<br />
+
+<ul>
+<li>copies all files and directories within orig_folder into new_folder (-r indicates this is a recursive copy, so all sub-directories and files within orig_folder will be included in new_folder)</li>
+</ul></li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td>man</td>
+<td><p>manual: displays documentation for commands</p>
+<p><strong>Note:</strong> Use up and down arrows to scroll through the text. To exit the manual display, press 'q'</p></td>
+<td><ul>
+<li>man <command name></li>
+<li>man ls
+<ul>
+<li>displays documentation for the ls command</li>
+</ul></li>
+</ul></td>
+</tr>
+<tr class="even">
+<td>mkdir</td>
+<td>make directory: creates a directory with the specified name</td>
+<td><ul>
+<li>mkdir <new_folder>
+<ul>
+<li>creates the directory "new_folder" within the current directory</li>
+</ul></li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td>rmdir</td>
+<td><p>remove directory: deletes a directory with the specified name</p>
+<p><strong>Note:</strong> rmdir only works on empty directories</p></td>
+<td><ul>
+<li>rmdir <folder_name>
+<ul>
+<li>removes the directory "folder_name" if the directory is empty</li>
+</ul></li>
+<li>rmdir *
+<ul>
+<li>removes all directories within the current directory</li>
+</ul></li>
+</ul></td>
+</tr>
+<tr class="even">
+<td>rm</td>
+<td>remove: deletes file or files with the specified name(s)</td>
+<td><ul>
+<li>rm <file_name>
+<ul>
+<li>deletes the file "file_name"</li>
+</ul></li>
+<li>rm *
+<ul>
+<li>deletes all files in the current directory</li>
+</ul></li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td><p>nano</p></td>
+<td><p>nano text editor: opens the nano text editor</p>
+<p><strong>Note:</strong> To access the menu options, ^ indicates the control (CTRL) key.</p></td>
+<td><ul>
+<li>nano
+<ul>
+<li>opens the text editor in a blank file</li>
+</ul></li>
+<li>nano <file_name>
+<ul>
+<li>opens the text editor with "file_name" open. If "file_name" does not exist, it will be created if the file is saved</li>
+</ul></li>
+</ul></td>
+</tr>
+<tr class="even">
+<td>clear</td>
+<td>clear: clears the screen of all input/output</td>
+<td><ul>
+<li>clear</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td>less</td>
+<td><p>less: opens an extended view of a file</p>
+<p><strong>Note:</strong> Use up and down arrows to scroll through the text. To exit the extended view, press 'q'</p></td>
+<td><ul>
+<li>less <file_name>
+<ul>
+<li>opens an extended view of the file "file_name"</li>
+</ul></li>
+</ul></td>
+</tr>
+<tr class="even">
+<td>cat</td>
+<td>concatenate: sends file contents to standard input - used frequently with pipes</td>
+<td><ul>
+<li>cat <file_name>
+<ul>
+<li>prints the contents of the file "file_name"</li>
+</ul></li>
+<li>cat *.txt
+<ul>
+<li>prints the contents of all files in the current directory that end in ".txt"</li>
+</ul></li>
+</ul></td>
+</tr>
+</tbody>
+</table>
+
+<span id="BashCommands-video" class="confluence-anchor-link"></span>
+
+Document generated by Confluence on Oct 24, 2018 14:47
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/quickstarts/condor_jobs_on_hcc.md b/content/quickstarts/condor_jobs_on_hcc.md
new file mode 100644
index 00000000..4fffe838
--- /dev/null
+++ b/content/quickstarts/condor_jobs_on_hcc.md
@@ -0,0 +1,264 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Quick Start Guides](Quick-Start-Guides_1245279.html)
+
+<span id="title-text"> HCC-DOCS : Condor Jobs on HCC </span>
+============================================================
+
+Created by <span class="author"> Huang Cheng-Wei</span>, last modified
+by <span class="editor"> Adam Caprez</span> on Sep 17, 2013
+
+This quick start demonstrates how to run multiple copies of<span
+style="font-size: 14.0px;line-height: 1.4285715;"> Fortran/C program
+using Condor on HCC supercomputers. The sample codes and submit scripts
+can be downloaded from
+<</span>[condor\_dir.zip](attachments/2851447/3178558.zip)<span
+style="font-size: 14.0px;line-height: 1.4285715;">>. </span>
+
+Login to Sandhills
+------------------
+
+Log in to Sandhills through PuTTY ([For Windows
+Users](For-Windows-Users_2851288.html)) or Terminal ([For Mac/Linux
+Users](2851290.html)) and make a subdirectory called condor\_dir under
+the `$WORK` directory. In the subdirectory `condor_dir`, create job
+subdirectories that host the input data files. Here we create two job
+subdirectories, `job_0` and `job_1`, and put a data file (`data.dat`) in
+each subdirectory. The data file in `job_0` has a column of data listing
+the integers from 1 to 5. The data file in `job_1` has a integer list
+from 6 to 10.
+
+``` syntaxhighlighter-pre
+$ cd $WORK
+$ mkdir condor_dir
+$ cd condor_dir
+$ mkdir job_0
+$ mkdir job_1
+```
+
+In the subdirectory condor`_dir`, save all the relevant codes. Here we
+include two demo programs, `demo_f_condor.f90` and `demo_c_condor.c`,
+that compute the sum of the data stored in each job subdirectory
+(`job_0` and `job_1`). The parallelization scheme here is as the
+following. First, the master computer node send out many copies of the
+executable from the `condor_dir` subdirectory and a copy of the data
+file in each job subdirectories. The number of executable copies is
+specified in the submit script (`queue`), and it usually matches with
+the number of job subdirectories. Next, the workload is distributed
+among a pool of worker computer nodes. At any given time, the number of
+available worker nodes may vary. Each worker node executes the jobs
+independent of other worker nodes. The output files are separately
+stored in the job subdirectory. No additional coding are needed to make
+the serial code turned "parallel". Parallelization here is achieved
+through the submit script.
+
+**demo\_f\_condor.f90** <span class="collapse-source expand-control"
+style="display:none;"><span
+class="expand-control-icon icon"> </span><span
+class="expand-control-text">Expand source</span></span> <span
+class="collapse-spinner-wrapper"></span>
+
+``` syntaxhighlighter-pre
+Program demo_f_condor
+ implicit none
+ integer, parameter :: N = 5
+ real*8 w
+ integer i
+ common/sol/ x
+ real*8 x
+ real*8, dimension(N) :: y_local
+ real*8, dimension(N) :: input_data
+
+ open(10, file='data.dat')
+
+ do i = 1,N
+ read(10,*) input_data(i)
+ enddo
+
+ do i = 1,N
+ w = input_data(i)*1d0
+ call proc(w)
+ y_local(i) = x
+ write(6,*) 'i,x = ', i, y_local(i)
+ enddo
+ write(6,*) 'sum(y) =',sum(y_local)
+Stop
+End Program
+Subroutine proc(w)
+ real*8, intent(in) :: w
+ common/sol/ x
+ real*8 x
+
+ x = w
+
+Return
+End Subroutine
+```
+
+**demo\_c\_condor.c** <span class="collapse-source expand-control"
+style="display:none;"><span
+class="expand-control-icon icon"> </span><span
+class="expand-control-text">Expand source</span></span> <span
+class="collapse-spinner-wrapper"></span>
+
+``` syntaxhighlighter-pre
+//demo_c_condor
+#include <stdio.h>
+
+double proc(double w){
+ double x;
+ x = w;
+ return x;
+}
+
+int main(int argc, char* argv[]){
+ int N=5;
+ double w;
+ int i;
+ double x;
+ double y_local[N];
+ double sum;
+ double input_data[N];
+ FILE *fp;
+ fp = fopen("data.dat","r");
+ for (i = 1; i<= N; i++){
+ fscanf(fp, "%lf", &input_data[i-1]);
+ }
+
+ for (i = 1; i <= N; i++){
+ w = input_data[i-1]*1e0;
+ x = proc(w);
+ y_local[i-1] = x;
+ printf("i,x= %d %lf\n", i, y_local[i-1]) ;
+ }
+
+ sum = 0e0;
+ for (i = 1; i<= N; i++){
+ sum = sum + y_local[i-1];
+ }
+
+ printf("sum(y)= %lf\n", sum);
+return 0;
+}
+```
+
+Compiling the Code
+------------------
+
+The compiled executable needs to match the "standard" environment of the
+worker node. The easies way is to directly use the compilers installed
+on the HCC supercomputer without loading extra modules. The standard
+compiler of the HCC supercomputer is GNU Compier Collection. The version
+can be looked up by the command lines `gcc -v` or `gfortran -v`.
+
+``` syntaxhighlighter-pre
+$ gfortran demo_f_condor.f90 -o demo_f_condor.x
+$ gcc demo_c_condor.c -o demo_c_condor.x
+```
+
+<span style="color: rgb(0,0,0);">Creating a Submit Script</span>
+----------------------------------------------------------------
+
+Create a submit script to request 2 jobs (queue). The name of the job
+subdirectories is specified in the line `initialdir`. The
+`$(process)` macro assigns integer numbers to the job subdirectory
+name `job_`. The numbers run form 0 to <span
+style="font-family: monospace;">queue-1</span>. The name of the input
+data file is specified in the line `transfer_input_files`.
+
+**submit\_f.condor**
+
+``` syntaxhighlighter-pre
+universe = grid
+grid_resource = pbs
+batch_queue = guest
+should_transfer_files = yes
+when_to_transfer_output = on_exit
+executable = demo_f_condor.x
+output = Fortran_$(process).out
+error = Fortran_$(process).err
+initialdir = job_$(process)
+transfer_input_files = data.dat
+queue 2
+```
+
+**submit\_c.condor**
+
+``` syntaxhighlighter-pre
+universe = grid
+grid_resource = pbs
+batch_queue = guest
+should_transfer_files = yes
+when_to_transfer_output = on_exit
+executable = demo_c_condor.x
+output = C_$(process).out
+error = C_$(process).err
+initialdir = job_$(process)
+transfer_input_files = data.dat
+queue 2
+```
+
+Submit the Job
+--------------
+
+The job can be submitted through the command `condor_submit`. The job
+status can be monitored by entering `condor_q` followed by the
+username.
+
+``` syntaxhighlighter-pre
+$ condor_submit submit_f.condor
+$ condor_submit submit_c.condor
+$ condor_q <username>
+```
+
+Sample Output
+-------------
+
+In the job subdirectory `job_0`, the sum from 1 to 5 is computed and
+printed to the `.out` file. In the job subdirectory `job_1`, the sum
+from 6 to 10 is computed and printed to the `.out` file.
+
+**Fortran\_0.out** <span class="collapse-source expand-control"
+style="display:none;"><span
+class="expand-control-icon icon"> </span><span
+class="expand-control-text">Expand source</span></span> <span
+class="collapse-spinner-wrapper"></span>
+
+``` syntaxhighlighter-pre
+ i,x = 1 1.0000000000000000
+ i,x = 2 2.0000000000000000
+ i,x = 3 3.0000000000000000
+ i,x = 4 4.0000000000000000
+ i,x = 5 5.0000000000000000
+ sum(y) = 15.000000000000000
+```
+
+**Fortran\_1.out** <span class="collapse-source expand-control"
+style="display:none;"><span
+class="expand-control-icon icon"> </span><span
+class="expand-control-text">Expand source</span></span> <span
+class="collapse-spinner-wrapper"></span>
+
+``` syntaxhighlighter-pre
+ i,x = 1 6.0000000000000000
+ i,x = 2 7.0000000000000000
+ i,x = 3 8.0000000000000000
+ i,x = 4 9.0000000000000000
+ i,x = 5 10.000000000000000
+ sum(y) = 40.000000000000000
+```
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[condor\_dir.zip](attachments/2851447/3178559.zip) (application/zip)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[condor\_dir.zip](attachments/2851447/3178560.zip) (application/zip)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[condor\_dir.zip](attachments/2851447/3178558.zip) (application/zip)
+
+Document generated by Confluence on Oct 24, 2018 14:47
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/quickstarts/for_maclinux_users.md b/content/quickstarts/for_maclinux_users.md
new file mode 100644
index 00000000..e76c7cf2
--- /dev/null
+++ b/content/quickstarts/for_maclinux_users.md
@@ -0,0 +1,207 @@
++++
+title = "For Mac/Linux Users"
+description = "Quickstart Guide for Mac/Linux Users"
++++
+
+
+<span id="title-text"> HCC-DOCS : For Mac/Linux Users </span>
+=============================================================
+
+Created by <span class="author"> Huang Cheng-Wei</span>, last modified
+by <span class="editor"> Caughlin Bohn</span> on Oct 26, 2017
+
+[Mac Tutorial Video](#ForMac/LinuxUsers-Video1)
+
+[Linux Tutorial Video](#ForMac/LinuxUsers-Video2)
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-warning confluence-information-macro-icon"></span>
+
+##### Use of Duo two-factor authentication is **required** to access HCC resources. Please see [Setting up and using Duo](Setting-up-and-using-Duo_5505155.html).
+
+
+
+This quick start will help you configure your personal computer to work
+with the HCC supercomputers.
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-warning confluence-information-macro-icon"></span>
+
+If you are running Windows, please use the quickstart [For Windows
+Users](For-Windows-Users_2851288.html).
+
+Accessing to HCC Supercomputers
+-------------------------------
+
+For Mac/Linux users, use the system program Terminal to assess to the
+HCC supercomputers. In the Terminal prompt,
+type `ssh <username>@tusker.unl.edu` and the corresponding password
+to get access to the HCC cluster **Tusker**. Note that <username>
+should be replaced by your HCC account username. If you do not have a
+HCC account, please contact a HCC specialist
+(<a href="mailto:hcc-support@unl.edu" class="external-link">hcc-support@unl.edu</a>)
+or go
+to <a href="http://hcc.unl.edu/newusers/" class="external-link">http://hcc.unl.edu/newusers/</a>. <span
+style="font-size: 14.0px;line-height: 1.4285715;">To use the **Crane**
+or </span>**Sandhills**<span
+style="font-size: 14.0px;line-height: 1.4285715;"> clusters, replace
+tusker.unl.edu </span><span
+style="font-size: 14.0px;line-height: 1.4285715;">with crane.unl.edu or
+sandhills.unl.edu</span><span
+style="font-size: 14.0px;line-height: 1.4285715;">. </span>
+
+``` syntaxhighlighter-pre
+$ ssh <username>@tusker.unl.edu
+$ <password>
+```
+
+
+
+File Transferring with HCC Supercomputers
+-----------------------------------------
+
+For Mac/Linux users, file transferring between your personal computer
+and the HCC supercomputers can be achieved through the commend `scp`.
+Here we use **Tusker** for example. **The following commands should be
+executed from your computer. **
+
+**Uploading from local to remote**
+
+``` syntaxhighlighter-pre
+$ scp -r ./<folder name> <username>@tusker.unl.edu:/work/<group name>/<username>
+```
+
+The above commend line transfers a folder from the current directory
+(`./`) of the your computer to the `$WORK` directory of the HCC
+supercomputer, Tusker. Note that you need to replace `<group name>`
+and `<username>` with your HCC group name and username.
+
+**Downloading from remote to local**
+
+``` syntaxhighlighter-pre
+$ scp -r <username>@tusker.unl.edu:/work/<group name>/<username>/<folder name> ./
+```
+
+The above commend line transfers a folder from the `$WORK` directory of
+the HCC supercomputer, Tusker, to the current directory (`./`) of the
+your computer.
+
+Using Cyberduck
+---------------
+
+If you wish to use a GUI, be aware that not all programs will function
+correctly with Duo two-factor authentication. Mac users are recommended
+to use Cyberduck
+(<a href="http://cyberduck.io" class="external-link">http://cyberduck.io</a>).
+ It is compatible with Duo, but a few settings need to be changed.
+
+Under **Preferences - General**, change the default protocol to SFTP:
+
+<span
+class="confluence-embedded-file-wrapper"><img src="assets/images/2851290/7274497.png" class="confluence-embedded-image" /></span>
+
+Under **Preferences - Transfers**, reuse the browser connection for file
+transfers. This will avoid the need to reenter your password for every
+file transfer:
+
+<span
+class="confluence-embedded-file-wrapper"><img src="assets/images/2851290/7274498.png" class="confluence-embedded-image" /></span>
+
+Finally, under **Preferences - SFTP**, set the file transfer method to
+SCP:
+
+<span
+class="confluence-embedded-file-wrapper"><img src="assets/images/2851290/7274499.png" class="confluence-embedded-image" /></span>
+
+To add an HCC machine, in the bookmarks pane click the "+" icon:
+
+<span
+class="confluence-embedded-file-wrapper"><img src="assets/images/2851290/7274500.png" class="confluence-embedded-image" /></span>
+
+<span style="line-height: 1.4285715;">Ensure the type of connection is
+SFTP. Enter the hostname of the machine you with to connect to
+(tusker.unl.edu, crane.unl.edu) in the </span>**Server**<span
+style="line-height: 1.4285715;"> field, and your HCC username in the
+</span>**Username**<span style="line-height: 1.4285715;"> field. The
+</span>**Nickname**<span style="line-height: 1.4285715;"> field is
+arbitrary, so enter whatever you prefer.</span>
+
+<span
+class="confluence-embedded-file-wrapper"><img src="assets/images/2851290/7274501.png" class="confluence-embedded-image" /></span>
+
+After you add the bookmark, double-click it to connect.
+
+<span
+class="confluence-embedded-file-wrapper"><img src="assets/images/2851290/7274505.png" class="confluence-embedded-image" /></span>
+
+Enter your HCC username and password in the dialog box that will appear
+and click *Login*.
+
+<span
+class="confluence-embedded-file-wrapper"><img src="assets/images/2851290/7274508.png" class="confluence-embedded-image" /></span>
+
+A second login dialogue will now appear. Notice the text has changed to
+say Duo two-factor.
+
+<span
+class="confluence-embedded-file-wrapper"><img src="assets/images/2851290/7274510.png" class="confluence-embedded-image" /></span>
+
+Clear the **Password** field in the dialogue. If you are using the Duo
+Mobile app, enter '1' to have a push notification send to your phone or
+tablet. If you are using a Yubikey, ensure the cursor is active in the
+**Password** field, and press the button on the Yubikey.
+
+<span
+class="confluence-embedded-file-wrapper"><img src="assets/images/2851290/7274509.png" class="confluence-embedded-image" /></span>
+
+The login should complete and you can simply drag and drop files to or
+from the window.
+
+<span
+class="confluence-embedded-file-wrapper"><img src="assets/images/2851290/7274511.png" class="confluence-embedded-image" /></span>
+
+<span id="ForMac/LinuxUsers-Video1"
+class="confluence-anchor-link"></span>
+
+ <span id="ForMac/LinuxUsers-Video2"
+class="confluence-anchor-link"></span>
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[osxfuse-2.5.6.dmg](attachments/2851290/3178535.dmg)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[Macfusion\_2.0.4.zip](attachments/2851290/3178536.zip)
+(application/zip)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[cyberduck1.png](attachments/2851290/7274497.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[cyberduck2.png](attachments/2851290/7274498.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[cyberduck3.png](attachments/2851290/7274499.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[cyberduck4.png](attachments/2851290/7274507.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[cyberduck5.png](attachments/2851290/7274501.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[cyberduck10.png](attachments/2851290/7274506.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[cyberduck10.png](attachments/2851290/7274505.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[cyberduck4.png](attachments/2851290/7274500.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[cyberduck11.png](attachments/2851290/7274508.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[cyberduck13.png](attachments/2851290/7274509.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[cyberduck12.png](attachments/2851290/7274510.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[cyberduck14.png](attachments/2851290/7274512.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[cyberduck14.png](attachments/2851290/7274511.png) (image/png)
+
+Document generated by Confluence on Oct 24, 2018 14:47
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/quickstarts/for_windows_users.md b/content/quickstarts/for_windows_users.md
new file mode 100644
index 00000000..996a63f2
--- /dev/null
+++ b/content/quickstarts/for_windows_users.md
@@ -0,0 +1,153 @@
++++
+title = "For Windows Users"
++++
+
+##### Use of Duo two-factor authentication is **required** to access HCC resources. Please see [Setting up and using Duo](Setting-up-and-using-Duo_5505155.html).
+
+
+This quick start will help you configure your personal computer to work
+with the HCC supercomputers. Here we use the two third party application
+**PuTTY** and **WinSCP** for demonstration.
+
+PuTTY:
+<a href="https://www.chiark.greenend.org.uk/~sgtatham/putty/latest.html" class="external-link">https://www.chiark.greenend.org.uk/~sgtatham/putty/latest.html</a>
+or <a href="https://the.earth.li/~sgtatham/putty/latest/w32/putty.exe" class="external-link">putty.exe</a>
+
+WinSCP:
+<a href="http://winscp.net/eng/download.php" class="external-link">http://winscp.net/eng/download.php</a>
+
+
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-warning confluence-information-macro-icon"></span>
+
+If you are on a Mac, please use the quickstart for [For Mac/Linux
+Users](2851290.html).
+
+Accessing to HCC Supercomputers
+-------------------------------
+
+Here we use the HCC cluster **Tusker** for demonstration. To use the
+**Crane** or **Sandhills** clusters, replace tusker.unl.edu with
+crane.unl.edu or sandhills.unl.edu.
+
+1. On the first screen, type `tusker.unl.edu` for Host Name, then click
+ **Open**.
+ <span
+ class="confluence-embedded-file-wrapper"><img src="assets/images/2851288/3178523.png" class="confluence-embedded-image" /></span>
+2. On the second screen, click on **Yes**.
+ <span
+ class="confluence-embedded-file-wrapper"><img src="assets/images/2851288/3178524.png" class="confluence-embedded-image" /></span>
+3. On the third screen, enter your HCC account **username**. If you do
+ not have a HCC account, please contact an HCC specialist
+ (<a href="mailto:hcc-support@unl.edu" class="external-link">hcc-support@unl.edu</a>)
+ or go to
+ <a href="http://hcc.unl.edu/newusers/" class="external-link">http://hcc.unl.edu/newusers/</a>.
+
+ <span
+ class="aui-icon aui-icon-small aui-iconfont-warning confluence-information-macro-icon"></span>
+ Replace `jingchao` with your username.
+
+
+ <span
+ class="confluence-embedded-file-wrapper"><img src="assets/images/2851288/8127261.png" class="confluence-embedded-image" /></span>
+
+
+
+4. On the next screen, enter your HCC account **password**.
+
+ <span
+ class="aui-icon aui-icon-small aui-iconfont-warning confluence-information-macro-icon"></span>
+ **Note that PuTTY will not show the characters as you type for
+ security reasons.**
+
+
+ <span
+ class="confluence-embedded-file-wrapper"><img src="assets/images/2851288/8127262.png" class="confluence-embedded-image" /></span>
+
+5. <span style="line-height: 1.4285715;">After you input the correct
+ password, you will be asked to choose a Duo authentication
+ method.</span>
+
+6. If you have a Yubikey set up by HCC, please hold the Yubikey for \~1
+ second. Then you will be brought to your home directory similar as
+ below.
+
+ <span
+ class="confluence-embedded-file-wrapper"><img src="assets/images/2851288/8127266.png" class="confluence-embedded-image" /></span>
+
+7. If you set up Duo via a smart phone, please type "1" in your
+ terminal and press "Enter". (Duo-Push is the most cost-effective way
+ for Duo authentication, we recommend all user use this option if
+ that is applicable.)
+
+8. Check your smart phone for Duo login request. Press "Approve" if you
+ can verify the request. If you find any Duo login request that is
+ not initiated by yourself, deny it and report this incident
+ immediately to hcc-support@unl.edu.
+
+ <span
+ class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/2851288/8127263.png" class="confluence-embedded-image confluence-thumbnail" width="300" /></span>
+
+9. After you approve the Duo login request, you will be brought to your
+ home directory similar as below.
+
+ <span
+ class="confluence-embedded-file-wrapper"><img src="assets/images/2851288/8127264.png" class="confluence-embedded-image" /></span>
+
+
+
+File Transferring with HCC Supercomputers
+-----------------------------------------
+
+Usually it is convenient <span
+style="font-size: 14.0px;line-height: 1.4285715;">to upload and download
+files between your personal computer and the HCC
+supercomputers </span><span
+style="font-size: 14.0px;line-height: 1.4285715;">through a Graphic User
+Interface (GUI). </span><span
+style="font-size: 14.0px;line-height: 1.4285715;">Download and
+install the third party application </span>**WinSCP**<span
+style="font-size: 14.0px;line-height: 1.4285715;"> </span><span
+style="font-size: 14.0px;line-height: 1.4285715;">to connect the file
+systems between your personal computer and the HCC supercomputers. Below
+is a step-by-step installation guide. Here we use the HCC
+cluster </span>**Tusker**<span
+style="font-size: 14.0px;line-height: 1.4285715;"> for demonstration. To
+use the </span>**Sandhills**<span
+style="font-size: 14.0px;line-height: 1.4285715;"> cluster, replace
+</span>`tusker.unl.edu`<span
+style="font-size: 14.0px;line-height: 1.4285715;"> for </span>`sandhills.unl.edu`<span
+style="font-size: 14.0px;line-height: 1.4285715;">.</span>
+
+1. On the first screen, type `tusker.unl.edu` for Host name, enter your
+ HCC account username and password for User name and Password. Then
+ click on **Login**.
+ <span
+ class="confluence-embedded-file-wrapper"><img src="assets/images/2851288/3178530.png" class="confluence-embedded-image" /></span>
+2. On the second screen, click on **Yes**.
+ <span
+ class="confluence-embedded-file-wrapper"><img src="assets/images/2851288/3178531.png" class="confluence-embedded-image" /></span>
+3. Choose option "1" and press "Enter". Or simply press your Yubikey if
+ you have one.
+
+ <span
+ class="confluence-embedded-file-wrapper"><img src="assets/images/2851288/8127268.png" class="confluence-embedded-image" /></span>
+4. On the third screen, click on **Remote**. Under Remote, choose Go To
+ and Open Directory/Bookmark. Alternatively, you can use the keyboard
+ shortcut "Ctrl + O".
+ <span
+ class="confluence-embedded-file-wrapper"><img src="assets/images/2851288/3178532.png" class="confluence-embedded-image" /></span>
+5. On the final screen, type `/work/<group name>/<username>` for Open
+ directory. Use your HCC group name and username to replace
+ `<group name>` and `<username>`. Then click on **OK**.
+ <span
+ class="confluence-embedded-file-wrapper"><img src="assets/images/2851288/3178533.png" class="confluence-embedded-image" /></span>
+6. Now you can drop and drag the files between your personal computer
+ and the HCC supercomputers.
+ <span
+ class="confluence-embedded-file-wrapper"><img src="assets/images/2851288/3178539.png" class="confluence-embedded-image" /></span>
+
+{{< youtube -Vh7SyC-3mA >}}
+
+
diff --git a/content/quickstarts/fortranc_on_hcc.md b/content/quickstarts/fortranc_on_hcc.md
new file mode 100644
index 00000000..678af560
--- /dev/null
+++ b/content/quickstarts/fortranc_on_hcc.md
@@ -0,0 +1,1559 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Quick Start Guides](Quick-Start-Guides_1245279.html)
+
+<span id="title-text"> HCC-DOCS : Fortran/C on HCC </span>
+==========================================================
+
+Created by <span class="author"> Huang Cheng-Wei</span>, last modified
+by <span class="editor"> Jingchao Zhang</span> on Dec 08, 2016
+
+This quick start demonstrates how to implement a Fortran/C program on
+HCC supercomputers. The sample codes and submit scripts can be
+downloaded from
+<[serial\_dir.zip](attachments/2851390/3178548.zip)>.
+
+Login to a HCC Cluster (Tusker or Sandhills)
+---------------------------------------------
+
+Log in to a HCC cluster through PuTTY ([For Windows
+Users](For-Windows-Users_2851288.html)) or Terminal ([For Mac/Linux
+Users](2851290.html)) and make a subdirectory called serial\_dir under
+the `$WORK` directory.
+
+``` syntaxhighlighter-pre
+$ cd $WORK
+$ mkdir serial_dir
+```
+
+In the subdirectory `serial_dir`, save all the relevant Fortran/C codes.
+Here we include two demo
+programs, `demo_f_serial.f90` and `demo_c_serial.c`, that compute the
+sum from 1 to 20.
+
+**demo\_f\_serial.f90** <span class="collapse-source expand-control"
+style="display:none;"><span
+class="expand-control-icon icon"> </span><span
+class="expand-control-text">Expand source</span></span> <span
+class="collapse-spinner-wrapper"></span>
+
+``` syntaxhighlighter-pre
+Program demo_f_serial
+ implicit none
+ integer, parameter :: N = 20
+ real*8 w
+ integer i
+ common/sol/ x
+ real*8 x
+ real*8, dimension(N) :: y
+
+ do i = 1,N
+ w = i*1d0
+ call proc(w)
+ y(i) = x
+ write(6,*) 'i,x = ', i, y(i)
+ enddo
+ write(6,*) 'sum(y) =',sum(y)
+Stop
+End Program
+Subroutine proc(w)
+ real*8, intent(in) :: w
+ common/sol/ x
+ real*8 x
+
+ x = w
+
+Return
+End Subroutine
+```
+
+**demo\_c\_serial.c** <span class="collapse-source expand-control"
+style="display:none;"><span
+class="expand-control-icon icon"> </span><span
+class="expand-control-text">Expand source</span></span> <span
+class="collapse-spinner-wrapper"></span>
+
+``` syntaxhighlighter-pre
+//demo_c_serial
+#include <stdio.h>
+
+double proc(double w){
+ double x;
+ x = w;
+ return x;
+}
+
+int main(int argc, char* argv[]){
+ int N=20;
+ double w;
+ int i;
+ double x;
+ double y[N];
+ double sum;
+ for (i = 1; i <= N; i++){
+ w = i*1e0;
+ x = proc(w);
+ y[i-1] = x;
+ printf("i,x= %d %lf\n", i, y[i-1]) ;
+ }
+
+ sum = 0e0;
+ for (i = 1; i<= N; i++){
+ sum = sum + y[i-1];
+ }
+
+ printf("sum(y)= %lf\n", sum);
+
+return 0;
+}
+```
+
+Compiling the Code
+------------------
+
+The compiling of a Fortran/C++ code to executable is usually done behind
+the scene in a Graphical User Interface (GUI) environment, such as
+Microsoft Visual Studio. In a HCC cluster, the compiling is done
+explicitly by first loading a choice compiler and then executing the
+corresponding compiling command. Here we will use the GNU Complier
+Collection, `gcc`, for demonstration. Other available compilers such as
+`intel` or `pgi` can be looked up using the command
+line `module avail`. <span
+style="font-size: 14.0px;line-height: 1.4285715;">Before compiling the
+code, make sure there is no dependency on any numerical library in the
+code. If invoking a numerical library is necessary, contact a HCC
+specialist
+(<a href="mailto:hcc-support@unl.edu" class="external-link">hcc-support@unl.edu</a>) to
+discuss implementation options. </span>
+
+| |
+|--------------------------------|
+| $ module load compiler/gcc/8.2 |
+
+$ gfortran demo\_f\_serial.f90 -o demo\_f\_serial.x
+$ gcc demo\_c\_serial.c -o demo\_c\_serial.x
+
+The above commends load the `gcc` complier and use the compiling
+commands `gfortran` or `gcc` to compile the codes to`.x` files
+(executables).
+
+Creating a Submit Script
+------------------------
+
+Create a submit script to request one core (default) and 1-min run time
+on the supercomputer. The name of the main program enters at the last
+line.
+
+**submit\_f.serial**
+
+``` syntaxhighlighter-pre
+#!/bin/sh
+#SBATCH --mem-per-cpu=1024
+#SBATCH --time=00:01:00
+#SBATCH --job-name=Fortran
+#SBATCH --error=Fortran.%J.err
+#SBATCH --output=Fortran.%J.out
+
+module load compiler/gcc/4.9
+./demo_f_serial.x
+```
+
+**submit\_c.serial**
+
+``` syntaxhighlighter-pre
+#!/bin/sh
+#SBATCH --mem-per-cpu=1024
+#SBATCH --time=00:01:00
+#SBATCH --job-name=C
+#SBATCH --error=C.%J.err
+#SBATCH --output=C.%J.out
+
+module load compiler/gcc/4.9
+./demo_c_serial.x
+```
+
+Submit the Job
+--------------
+
+The job can be submitted through the command `sbatch`. The job status
+can be monitored by entering `squeue` with the `-u` option.
+
+``` syntaxhighlighter-pre
+$ sbatch submit_f.serial
+$ sbatch submit_c.serial
+$ squeue -u <username>
+```
+
+Sample Output
+-------------
+
+The sum from 1 to 20 is computed and printed to the `.out` file (see
+below).
+
+**Fortran.out** <span class="collapse-source expand-control"
+style="display:none;"><span
+class="expand-control-icon icon"> </span><span
+class="expand-control-text">Expand source</span></span> <span
+class="collapse-spinner-wrapper"></span>
+
+``` syntaxhighlighter-pre
+ i,x = 1 1.0000000000000000
+ i,x = 2 2.0000000000000000
+ i,x = 3 3.0000000000000000
+ i,x = 4 4.0000000000000000
+ i,x = 5 5.0000000000000000
+ i,x = 6 6.0000000000000000
+ i,x = 7 7.0000000000000000
+ i,x = 8 8.0000000000000000
+ i,x = 9 9.0000000000000000
+ i,x = 10 10.000000000000000
+ i,x = 11 11.000000000000000
+ i,x = 12 12.000000000000000
+ i,x = 13 13.000000000000000
+ i,x = 14 14.000000000000000
+ i,x = 15 15.000000000000000
+ i,x = 16 16.000000000000000
+ i,x = 17 17.000000000000000
+ i,x = 18 18.000000000000000
+ i,x = 19 19.000000000000000
+ i,x = 20 20.000000000000000
+ sum(y) = 210.00000000000000
+```
+
+**C.out** <span class="collapse-source expand-control"
+style="display:none;"><span
+class="expand-control-icon icon"> </span><span
+class="expand-control-text">Expand source</span></span> <span
+class="collapse-spinner-wrapper"></span>
+
+``` syntaxhighlighter-pre
+i,x= 1 1.000000
+i,x= 2 2.000000
+i,x= 3 3.000000
+i,x= 4 4.000000
+i,x= 5 5.000000
+i,x= 6 6.000000
+i,x= 7 7.000000
+i,x= 8 8.000000
+i,x= 9 9.000000
+i,x= 10 10.000000
+i,x= 11 11.000000
+i,x= 12 12.000000
+i,x= 13 13.000000
+i,x= 14 14.000000
+i,x= 15 15.000000
+i,x= 16 16.000000
+i,x= 17 17.000000
+i,x= 18 18.000000
+i,x= 19 19.000000
+i,x= 20 20.000000
+sum(y)= 210.000000
+```
+
+
+
+
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[serial\_dir.zip](attachments/2851390/3178549.zip) (application/zip)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[serial\_dir.zip](attachments/2851390/3178550.zip) (application/zip)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[serial\_dir.zip](attachments/2851390/3178551.zip) (application/zip)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[serial\_dir.zip](attachments/2851390/3178552.zip) (application/zip)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[serial\_dir.zip](attachments/2851390/3178554.zip) (application/zip)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[serial\_dir.zip](attachments/2851390/3178556.zip) (application/zip)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[serial\_dir.zip](attachments/2851390/3178548.zip) (application/zip)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/2851390/8127337.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/2851390/8127407.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/2851390/8127662.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[cb\_fortran\_qsg.xsl](attachments/2851390/8127415.xsl)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/2851390/8127738.xml)
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/2851390/8945692.xml)
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/2851390/8945726.xml)
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+[tusker\_modules.xml](attachments/2851390/9863230.xml)
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+[tusker\_modules.xml](attachments/2851390/11633635.xml)
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/2851390/30449021.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/2851390/33685582.xml)
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+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/2851390/33685693.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/2851390/33685805.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/2851390/33685910.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/2851390/33686047.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/2851390/33686151.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/2851390/33686290.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/2851390/33687826.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/2851390/33688433.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/2851390/33689759.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/2851390/33689979.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/2851390/35324019.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/2851390/35324129.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/2851390/35324599.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/2851390/35324889.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/2851390/35325621.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/2851390/35325734.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/2851390/35326721.xml)
+(application/octet-stream)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/2851390/8127216.xml)
+(application/octet-stream)
+
+Document generated by Confluence on Oct 24, 2018 14:47
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/quickstarts/how_to_change_your_password.md b/content/quickstarts/how_to_change_your_password.md
new file mode 100644
index 00000000..0fde8058
--- /dev/null
+++ b/content/quickstarts/how_to_change_your_password.md
@@ -0,0 +1,132 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Quick Start Guides](Quick-Start-Guides_1245279.html)
+
+<span id="title-text"> HCC-DOCS : How to change your password </span>
+=====================================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified by
+<span class="editor"> Carrie Brown</span> on Oct 24, 2018
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-info confluence-information-macro-icon"></span>
+
+Your account must be active with Duo authentication setup in order for
+the following instructions to work.
+
+- [HCC password
+ requirements](#Howtochangeyourpassword-HCCpasswordrequirements)
+- [Changing a known HCC
+ password](#Howtochangeyourpassword-ChangingaknownHCCpassword)
+ - [Change your password via the command
+ line](#Howtochangeyourpassword-Changeyourpasswordviathecommandline)
+ - [Change your password using the myHCC User
+ Portal](#Howtochangeyourpassword-ChangeyourpasswordusingthemyHCCUserPortal)
+- [Resetting a forgotten HCC
+ password](#Howtochangeyourpassword-ResettingaforgottenHCCpassword)
+- [Tutorial Video](#Howtochangeyourpassword-TutorialVideo)
+
+Every HCC user has a password that is same on all HCC machines
+(Sandhills, Tusker, Crane). This password needs to satisfy the HCC
+password requirements.<span style="line-height: 1.42857;"> </span>
+
+### **HCC password requirements**
+
+All HCC passwords must meet the following requirements when they are
+created or changed:
+
+- at least 8 characters long
+- at least 1 capital letter
+- at least 1 number
+- **can not**<span style="line-height: 1.42857;"> contain an existing
+ dictionary word</span>
+- **can not**<span style="line-height: 1.42857;"> contain information
+ from user's account details (</span>*username*<span
+ style="line-height: 1.42857;">, </span>*email*<span
+ style="line-height: 1.42857;">)</span>
+
+Using special characters in the password is not required, but it is
+allowed. Also, the system keeps a history of the user's previous two
+passwords, and their reuse is not allowed.
+
+### **Changing a known HCC password**
+
+If you know your current HCC password, you can use one of two approaches
+to change it:
+
+#### **Change your password via the command line **
+
+To change a current or temporary password, the user needs to login to
+any HCC cluster (Crane or Tusker) and use the ***passwd*** command:
+
+**Change HCC password**
+
+``` syntaxhighlighter-pre
+$ passwd
+Changing password for user <username>.
+Current Password:
+New password:
+New password:
+```
+
+With this command, the user is first prompted for his/her old password.
+If the "*Current Password*" is correct, then the user is asked twice for
+a replacement password ("*New password*"). The replacement password
+needs to fulfill the HCC password requirements.
+
+#### Change your password using the myHCC User Portal
+
+1. Login to the
+ <a href="https://hcc.unl.edu/myhcc/" class="external-link">myHCC User Portal</a>
+ with your HCC credentials.
+2. Click **Update Account** in the top menu
+
+ <span
+ class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/13041705/35326617.png" class="confluence-embedded-image image-center" height="150" /></span>
+
+3. Enter your new password in the **Password** and **Retype Password**
+ boxes and click **Modify** to save
+
+<span
+class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/13041705/35326618.png" class="confluence-embedded-image image-center" height="150" /></span>
+
+### **Resetting a forgotten HCC password**
+
+To reset your password, navigate to the
+<a href="https://hcc.unl.edu/myhcc/" class="external-link">myHCC User Portal</a>
+in your browser
+
+Click the link to reset your forgotten password
+
+<span
+class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/13041705/35326619.png" class="confluence-embedded-image image-center" height="400" /></span>
+
+Fill in the requested information (your HCC user name and email
+associated with your account) and click **Reset Password**. A reset link
+will be sent to your email address. Click this link and follow the
+onscreen prompts to set a new password.
+
+### Tutorial Video
+
+
+
+<span id="Howtochangeyourpassword-Video"
+class="confluence-anchor-link"></span>
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2018-10-18\_13-25-46.png](attachments/13041705/35326617.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2018-10-18\_13-27-34.png](attachments/13041705/35326618.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2018-10-18\_13-31-22.png](attachments/13041705/35326619.png)
+(image/png)
+
+Document generated by Confluence on Oct 24, 2018 14:47
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/quickstarts/how_to_setup_x11_forwarding.md b/content/quickstarts/how_to_setup_x11_forwarding.md
new file mode 100644
index 00000000..0b004e26
--- /dev/null
+++ b/content/quickstarts/how_to_setup_x11_forwarding.md
@@ -0,0 +1,102 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Quick Start Guides](Quick-Start-Guides_1245279.html)
+
+<span id="title-text"> HCC-DOCS : How to setup X11 forwarding </span>
+=====================================================================
+
+Created by <span class="author"> Jingchao Zhang</span>, last modified by
+<span class="editor"> Adam Caprez</span> on Jun 20, 2018
+
+If you are connecting to HCC clusters via a PC running Windows, please take the following steps to setup X11 forwarding.
+------------------------------------------------------------------------------------------------------------------------
+
+1. Download Xming to your local PC and install. Download
+ link: <a href="http://sourceforge.net/project/downloading.php?group_id=156984&filename=Xming-6-9-0-31-setup.exe" class="external-link">http://sourceforge.net/project/downloading.php?group_id=156984&filename=Xming-6-9-0-31-setup.exe</a>
+2. Download PuTTY to your local PC and install. Download
+ link: <a href="http://the.earth.li/~sgtatham/putty/latest/x86/putty.exe" class="external-link">http://the.earth.li/~sgtatham/putty/latest/x86/putty.exe</a>
+3. Open Xming and keep it running in the background.
+4. Configure PuTTY as below:
+ <span
+ class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/11637375/11637370.png" class="confluence-embedded-image" height="400" /></span><span
+ class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/11637375/11637371.jpg" class="confluence-embedded-image" height="400" /></span>
+5. To test your X11 setup, after login, type command "xeyes" and press
+ enter.
+ <span
+ class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/11637375/11637372.png" class="confluence-embedded-image" height="400" /></span>
+6. Close the xeyes application by "Ctrl + c" from the terminal or click
+ the close button on the up-right corner of the graphical window.
+
+
+
+If you are connecting to HCC clusters via a Macintosh, please take the following steps to setup X11 forwarding.
+---------------------------------------------------------------------------------------------------------------
+
+- <span style="color: rgb(51,51,51);font-size: 14.0px;line-height: 1.42857;">Check the OS version on your Mac, if it's below 10.8., you can simply type "ssh -Y username@hostname" in your terminal to login.</span>
+ ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+
+ <span
+ style="color: rgb(51,51,51);font-size: 14.0px;line-height: 1.42857;">
+ </span>
+
+- If your OS version is newer than 10.8, please do the following:
+
+1. Download and install XQuartz.
+ Download link: <a href="http://xquartz.macosforge.org/downloads/SL/XQuartz-2.7.7.dmg" class="external-link">http://xquartz.macosforge.org/downloads/SL/XQuartz-2.7.7.dmg</a>
+2. Type "ssh -Y username@hostname" in your terminal to login.
+3. To test your X11 setup, after login, type command "xeyes" and press
+ enter.
+ <span
+ class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/11637375/11637374.png" class="confluence-embedded-image" height="400" /></span>
+4. Close the xeyes application by "control + c" from the terminal or
+ click the close button on the up-left corner of the graphical
+ window.
+
+
+If you are connecting to HCC clusters via a Linux laptop, please take the following steps to setup X11 forwarding.
+------------------------------------------------------------------------------------------------------------------
+
+1. Open the remote client terminal.
+2. Type "ssh -Y username@hostname" in your terminal to login.
+3. To test your X11 setup, after login, type command "xeyes" and press
+ enter.
+4. Close the xeyes application by "Ctrl + c" from the terminal or click
+ the close button on the up-right corner of the graphical window.
+
+
+
+Related articles
+----------------
+
+<a href="http://www.straightrunning.com/XmingNotes/" class="external-link">X11 on Windows</a>
+
+<a href="https://en.wikipedia.org/wiki/XQuartz" class="external-link">X11 on Mac</a>
+
+<a href="http://www.wikihow.com/Configure-X11-in-Linux" class="external-link">X11 on Linux</a>
+
+
+
+
+
+
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[PuTTY\_1.jpg](attachments/11637375/11637369.jpg) (image/jpeg)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[PuTTY\_1.jpg](attachments/11637375/11637368.jpg) (image/jpeg)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[PuTTY\_1.png](attachments/11637375/11637370.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[PuTTY\_2.jpg](attachments/11637375/11637371.jpg) (image/jpeg)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[PuTTY\_3.png](attachments/11637375/11637372.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[max\_02.png](attachments/11637375/11637374.png) (image/png)
+
+Document generated by Confluence on Oct 24, 2018 14:47
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/quickstarts/mpi_jobs_on_hcc.md b/content/quickstarts/mpi_jobs_on_hcc.md
new file mode 100644
index 00000000..7a544feb
--- /dev/null
+++ b/content/quickstarts/mpi_jobs_on_hcc.md
@@ -0,0 +1,1645 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Quick Start Guides](Quick-Start-Guides_1245279.html)
+
+<span id="title-text"> HCC-DOCS : MPI Jobs on HCC </span>
+=========================================================
+
+Created by <span class="author"> Huang Cheng-Wei</span>, last modified
+by <span class="editor"> Natasha Pavlovikj</span> on Dec 07, 2017
+
+This quick start demonstrates how to implement a parallel (MPI)
+Fortran/C program on HCC supercomputers. The sample codes and submit
+scripts can be downloaded from
+<[mpi\_dir.zip](attachments/2851393/3178553.zip)>.
+
+Login to a HCC Cluster
+----------------------
+
+Log in to a HCC cluster through PuTTY ([For Windows
+Users](For-Windows-Users_2851288.html)) or Terminal ([For Mac/Linux
+Users](2851290.html)) and make a subdirectory called mpi\_dir under
+the `$WORK` directory.
+
+``` syntaxhighlighter-pre
+$ cd $WORK
+$ mkdir mpi_dir
+```
+
+In the subdirectory `mpi_dir`, save all the relevant codes. Here we
+include two demo programs, `demo_f_mpi.f90` and `demo_c_mpi.c`, that
+compute the sum from 1 to 20 through parallel processes. A
+straightforward parallelization scheme is used for demonstration
+purpose. First, the master core (i.e. `myid=0`) distributes equal
+computation workload to a certain number of cores (as specified by
+`--ntasks `in the submit script). Then, each worker core computes a
+partial summation as output. Finally, the master core collects the
+outputs from all worker cores and perform an overall summation. For easy
+comparison with the serial code ([Fortran/C on HCC](2851390.html)), the
+added lines in the parallel code (MPI) are marked with "!=" or "//=".
+
+**demo\_f\_mpi.f90** <span class="collapse-source expand-control"
+style="display:none;"><span
+class="expand-control-icon icon"> </span><span
+class="expand-control-text">Expand source</span></span> <span
+class="collapse-spinner-wrapper"></span>
+
+``` syntaxhighlighter-pre
+Program demo_f_mpi
+!====== MPI =====
+ use mpi
+!================
+ implicit none
+ integer, parameter :: N = 20
+ real*8 w
+ integer i
+ common/sol/ x
+ real*8 x
+ real*8, dimension(N) :: y
+!============================== MPI =================================
+ integer ind
+ real*8, dimension(:), allocatable :: y_local
+ integer numnodes,myid,rc,ierr,start_local,end_local,N_local
+ real*8 allsum
+!====================================================================
+
+!============================== MPI =================================
+ call mpi_init( ierr )
+ call mpi_comm_rank ( mpi_comm_world, myid, ierr )
+ call mpi_comm_size ( mpi_comm_world, numnodes, ierr )
+ !
+ N_local = N/numnodes
+ allocate ( y_local(N_local) )
+ start_local = N_local*myid + 1
+ end_local = N_local*myid + N_local
+!====================================================================
+ do i = start_local, end_local
+ w = i*1d0
+ call proc(w)
+ ind = i - N_local*myid
+ y_local(ind) = x
+! y(i) = x
+! write(6,*) 'i, y(i)', i, y(i)
+ enddo
+! write(6,*) 'sum(y) =',sum(y)
+!============================================== MPI =====================================================
+ call mpi_reduce( sum(y_local), allsum, 1, mpi_real8, mpi_sum, 0, mpi_comm_world, ierr )
+ call mpi_gather ( y_local, N_local, mpi_real8, y, N_local, mpi_real8, 0, mpi_comm_world, ierr )
+
+ if (myid == 0) then
+ write(6,*) '-----------------------------------------'
+ write(6,*) '*Final output from... myid=', myid
+ write(6,*) 'numnodes =', numnodes
+ write(6,*) 'mpi_sum =', allsum
+ write(6,*) 'y=...'
+ do i = 1, N
+ write(6,*) y(i)
+ enddo
+ write(6,*) 'sum(y)=', sum(y)
+ endif
+
+ deallocate( y_local )
+ call mpi_finalize(rc)
+!========================================================================================================
+
+Stop
+End Program
+Subroutine proc(w)
+ real*8, intent(in) :: w
+ common/sol/ x
+ real*8 x
+
+ x = w
+
+Return
+End Subroutine
+```
+
+**demo\_c\_mpi.c** <span class="collapse-source expand-control"
+style="display:none;"><span
+class="expand-control-icon icon"> </span><span
+class="expand-control-text">Expand source</span></span> <span
+class="collapse-spinner-wrapper"></span>
+
+``` syntaxhighlighter-pre
+//demo_c_mpi
+#include <stdio.h>
+//======= MPI ========
+#include "mpi.h"
+#include <stdlib.h>
+//====================
+
+double proc(double w){
+ double x;
+ x = w;
+ return x;
+}
+
+int main(int argc, char* argv[]){
+ int N=20;
+ double w;
+ int i;
+ double x;
+ double y[N];
+ double sum;
+//=============================== MPI ============================
+ int ind;
+ double *y_local;
+ int numnodes,myid,rc,ierr,start_local,end_local,N_local;
+ double allsum;
+//================================================================
+//=============================== MPI ============================
+ MPI_Init(&argc, &argv);
+ MPI_Comm_rank( MPI_COMM_WORLD, &myid );
+ MPI_Comm_size ( MPI_COMM_WORLD, &numnodes );
+ N_local = N/numnodes;
+ y_local=(double *) malloc(N_local*sizeof(double));
+ start_local = N_local*myid + 1;
+ end_local = N_local*myid + N_local;
+//================================================================
+
+ for (i = start_local; i <= end_local; i++){
+ w = i*1e0;
+ x = proc(w);
+ ind = i - N_local*myid;
+ y_local[ind-1] = x;
+// y[i-1] = x;
+// printf("i,x= %d %lf\n", i, y[i-1]) ;
+ }
+ sum = 0e0;
+ for (i = 1; i<= N_local; i++){
+ sum = sum + y_local[i-1];
+ }
+// printf("sum(y)= %lf\n", sum);
+//====================================== MPI ===========================================
+ MPI_Reduce( &sum, &allsum, 1, MPI_DOUBLE, MPI_SUM, 0, MPI_COMM_WORLD );
+ MPI_Gather( &y_local[0], N_local, MPI_DOUBLE, &y[0], N_local, MPI_DOUBLE, 0, MPI_COMM_WORLD );
+
+ if (myid == 0){
+ printf("-----------------------------------\n");
+ printf("*Final output from... myid= %d\n", myid);
+ printf("numnodes = %d\n", numnodes);
+ printf("mpi_sum = %lf\n", allsum);
+ printf("y=...\n");
+ for (i = 1; i <= N; i++){
+ printf("%lf\n", y[i-1]);
+ }
+ sum = 0e0;
+ for (i = 1; i<= N; i++){
+ sum = sum + y[i-1];
+ }
+
+ printf("sum(y) = %lf\n", sum);
+
+ }
+
+ free( y_local );
+ MPI_Finalize ();
+//======================================================================================
+
+return 0;
+}
+```
+
+Compiling the Code
+------------------
+
+The compiling of a MPI code requires first loading a compiler "engine"
+such as `gcc`, `intel`, or `pgi` and then loading a MPI wrapper
+`openmpi`. Here we will use the GNU Complier Collection, `gcc`, for
+demonstration.
+
+module load compiler/gcc/6.1 openmpi/2.1
+
+$ mpif90 demo\_f\_mpi.f90 -o demo\_f\_mpi.x
+$ mpicc demo\_c\_mpi.c -o demo\_c\_mpi.x
+
+
+
+The above commends load the `gcc` complier with the `openmpi` wrapper.
+The compiling commands `mpif90` or `mpicc` are used to compile the codes
+to`.x` files (executables).
+
+
+
+<span
+style="color: rgb(0,0,0);font-size: 20.0px;line-height: 1.5;">Creating a
+Submit Script</span>
+
+Create a submit script to request 5 cores (with `--ntasks`). A parallel
+execution command `mpirun ./` needs to enter to last line before the
+main program name.
+
+**submit\_f.mpi**
+
+``` syntaxhighlighter-pre
+#!/bin/sh
+#SBATCH --ntasks=5
+#SBATCH --mem-per-cpu=1024
+#SBATCH --time=00:01:00
+#SBATCH --job-name=Fortran
+#SBATCH --error=Fortran.%J.err
+#SBATCH --output=Fortran.%J.out
+
+mpirun ./demo_f_mpi.x
+```
+
+**submit\_c.mpi**
+
+``` syntaxhighlighter-pre
+#!/bin/sh
+#SBATCH --ntasks=5
+#SBATCH --mem-per-cpu=1024
+#SBATCH --time=00:01:00
+#SBATCH --job-name=C
+#SBATCH --error=C.%J.err
+#SBATCH --output=C.%J.out
+
+mpirun ./demo_c_mpi.x
+```
+
+Submit the Job
+--------------
+
+The job can be submitted through the command `sbatch`. The job status
+can be monitored by entering `squeue` with the `-u` option.
+
+``` syntaxhighlighter-pre
+$ sbatch submit_f.mpi
+$ sbatch submit_c.mpi
+$ squeue -u <username>
+```
+
+Sample Output
+-------------
+
+The sum from 1 to 20 is computed and printed to the `.out` file (see
+below). The outputs from the 5 cores are collected and processed by the
+master core (i.e. `myid=0`).
+
+**Fortran.out** <span class="collapse-source expand-control"
+style="display:none;"><span
+class="expand-control-icon icon"> </span><span
+class="expand-control-text">Expand source</span></span> <span
+class="collapse-spinner-wrapper"></span>
+
+``` syntaxhighlighter-pre
+ -----------------------------------------
+ *Final output from... myid= 0
+ numnodes = 5
+ mpi_sum = 210.00000000000000
+ y=...
+ 1.0000000000000000
+ 2.0000000000000000
+ 3.0000000000000000
+ 4.0000000000000000
+ 5.0000000000000000
+ 6.0000000000000000
+ 7.0000000000000000
+ 8.0000000000000000
+ 9.0000000000000000
+ 10.000000000000000
+ 11.000000000000000
+ 12.000000000000000
+ 13.000000000000000
+ 14.000000000000000
+ 15.000000000000000
+ 16.000000000000000
+ 17.000000000000000
+ 18.000000000000000
+ 19.000000000000000
+ 20.000000000000000
+ sum(y)= 210.00000000000000
+
+```
+
+**C.out** <span class="collapse-source expand-control"
+style="display:none;"><span
+class="expand-control-icon icon"> </span><span
+class="expand-control-text">Expand source</span></span> <span
+class="collapse-spinner-wrapper"></span>
+
+``` syntaxhighlighter-pre
+-----------------------------------
+*Final output from... myid= 0
+numnodes = 5
+mpi_sum = 210.000000
+y=...
+1.000000
+2.000000
+3.000000
+4.000000
+5.000000
+6.000000
+7.000000
+8.000000
+9.000000
+10.000000
+11.000000
+12.000000
+13.000000
+14.000000
+15.000000
+16.000000
+17.000000
+18.000000
+19.000000
+20.000000
+sum(y) = 210.000000
+```
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[mpi\_dir.zip](attachments/2851393/3178555.zip) (application/zip)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[mpi\_dir.zip](attachments/2851393/3178557.zip) (application/zip)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[mpi\_dir.zip](attachments/2851393/3178553.zip) (application/zip)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[tusker\_modules.xml](attachments/2851393/8127338.xml)
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+
+Document generated by Confluence on Oct 24, 2018 14:47
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/quickstarts/reusing_ssh_connections_in_linux_or_mac.md b/content/quickstarts/reusing_ssh_connections_in_linux_or_mac.md
new file mode 100644
index 00000000..05650ba6
--- /dev/null
+++ b/content/quickstarts/reusing_ssh_connections_in_linux_or_mac.md
@@ -0,0 +1,40 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Quick Start Guides](Quick-Start-Guides_1245279.html)
+
+<span id="title-text"> HCC-DOCS : Reusing SSH connections in Linux/Mac </span>
+==============================================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified by
+<span class="editor"> Derek Weitzel</span> on Feb 27, 2014
+
+To make it more convenient for users who use multiple terminal sessions
+simultaneously, SSH can reuse an existing connection if connecting from
+Linux or Mac. After the initial login, subsequent terminals can use
+that connection, eliminating the need to enter the username and password
+each time for every connection. To enable this feature, add the
+following lines to your `~/.ssh/config `file:
+
+**\~/.ssh/config**
+
+``` syntaxhighlighter-pre
+Host *
+ControlMaster auto
+ControlPath /tmp/%r@%h:%p
+ControlPersist 2h
+```
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-info confluence-information-macro-icon"></span>
+
+You may not have an existing `~/.ssh/config.` If not, simply create the
+file and set the permissions appropriately first:
+`touch ~/.ssh/config && chmod 600 ~/.ssh/config`
+
+This will enable connection reuse when connecting to any host via SSH or
+SCP.
+
+Document generated by Confluence on Oct 24, 2018 14:47
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/quickstarts/setting_up_and_using_duo.md b/content/quickstarts/setting_up_and_using_duo.md
new file mode 100644
index 00000000..8041b7b1
--- /dev/null
+++ b/content/quickstarts/setting_up_and_using_duo.md
@@ -0,0 +1,212 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Quick Start Guides](Quick-Start-Guides_1245279.html)
+
+<span id="title-text"> HCC-DOCS : Setting up and using Duo </span>
+==================================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified on
+Sep 18, 2018
+
+**Use of Duo two-factor authentication
+(<a href="https://www.duosecurity.com" class="external-link">https://www.duosecurity.com</a>)
+is required for access to HCC resources.** Users will connect via SSH
+and enter their username/passwords as usual. One additional
+authentication step through Duo is then needed before the login is
+completed. This second authentication can be in several different forms
+(cell phone, YubiKey hardware token), and is user-selectable at each
+login. A brief description of each is provided
+[below](#SettingupandusingDuo-authmethods). See
+the <a href="https://www.duosecurity.com/authentication-methods" class="external-link">Duo Authentication Methods</a>
+page for more details.
+
+Initial Setup
+=============
+
+Most HCC account holders use the Duo Mobile application on their
+smartphone or purchase a YubiKey USB device.
+
+<span style="color: rgb(0,0,0);">Smartphone</span>
+--------------------------------------------------
+
+1. Install the free *Duo Mobile* application from the
+ <a href="https://play.google.com/store/apps/details?id=com.duosecurity.duomobile" class="external-link">Google Play Store</a>, <a href="https://itunes.apple.com/us/app/duo-mobile/id422663827" class="external-link">Apple App Store</a> or <a href="https://www.microsoft.com/en-us/store/apps/duo-mobile/9nblggh08m1g" class="external-link">Microsoft Store</a>.
+2. Visit one of the following locations. **Bring your smartphone and a
+ valid photo ID** such as your university ID card or drivers license.
+ 1. Visit either HCC location
+ (<a href="http://www1.unl.edu/tour/SHOR" class="external-link">118 Schorr Center, UNL</a> \|\| <a href="http://pki.nebraska.edu/new/pages/about-pki/maps-directions-and-parking/" class="external-link">152 Peter Kiewit Institute, UNO</a>) in-person
+ anytime from 9am-5pm to enroll.
+ 2. Visit Information Technology Services
+ <a href="http://www.unk.edu/campus-map/?q=m15" class="external-link">107 Otto Olsen, UNK</a>
+ in-person and ask for HCC identity verification.
+
+Faculty/staff members with a verified NU telephone number can enroll by
+phone. If you would like an HCC staff member to call your NU telephone
+number to enroll, please email
+<a href="mailto:hcc-support@unl.edu" class="external-link">hcc-support@unl.edu</a>
+with a time you will be available.
+
+YubiKeys
+--------
+
+YubiKey devices are currently a one-time cost of $22 from HCC, or can be
+purchased from Yubico and added in-person at either HCC location.
+Purchasing a YubiKey from HCC must be done via a University cost object
+transfer (HCC cannot accept cash or credit cards). Please bring the cost
+object number with you if possible. YubiKeys are available from the
+Union Bookstore at UNL for a one-time cost of $25 each. Note that
+YubiKeys are configured for HCC's Duo, and not for general YubiCloud or
+U2F use.
+
+Example login using Duo Push
+============================
+
+This demonstrates an example login to Crane using the Duo Push method.
+Using another method (SMS, phone call, etc.) proceeds in the same way.
+ (Click on any image for a larger version.)
+
+First, a user connects via SSH using their normal HCC username/password,
+exactly as before.
+
+<span
+class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/5505155/5832713.png" class="confluence-embedded-image image-center" width="500" /></span>
+
+Account lockout
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-warning confluence-information-macro-icon"></span>
+
+**After 10 failed authentication attempts, the user's account is
+disabled. If this is the case, then the user needs to send an email to
+<a href="mailto:hcc-support@unl.edu" class="external-link">hcc-support@unl.edu</a>
+including his/her username and the reason why multiple failed
+authentication attempts occurred.
+**
+
+After entering the password, instead of completing the login, the user
+will be presented with the Duo prompt. This gives the choice to use any
+authentication method that the particular account is setup to use. In
+this example, the choices are Duo Push notification, SMS message, or
+phone call. Choosing option 1 for Duo Push, a request to verify the
+login will be sent to the user's smartphone.
+
+<span
+class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/5505155/5832716.png" class="confluence-embedded-image confluence-content-image-border image-center" width="100" height="178" /></span>
+
+Simply tap `Approve` to verify the login.
+
+<span
+class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/5505155/5832717.png" class="confluence-embedded-image confluence-content-image-border image-center" width="100" height="178" /></span>
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-warning confluence-information-macro-icon"></span>
+
+**If you receive a verification request you didn't initiate, deny the
+request and contact HCC immediately via email at
+<a href="mailto:hcc-support@unl.edu" class="external-link">hcc-support@unl.edu</a>.
+**
+
+In the terminal, the login will now complete and the user will logged in
+as usual.
+
+<span
+class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/5505155/5832714.png" class="confluence-embedded-image confluence-thumbnail image-center" width="300" /></span>
+
+
+
+<span id="SettingupandusingDuo-authmethods" class="confluence-anchor-link"></span>Duo Authentication Methods
+============================================================================================================
+
+### <span style="color: rgb(0,0,0);font-size: 16.0px;line-height: 1.5625;">Duo Push</span><span style="color: rgb(0,0,0);font-size: 16.0px;line-height: 1.5625;"> </span><span style="line-height: 1.5625;"> \[</span><a href="https://www.duosecurity.com/duo-push" class="external-link"><span style="line-height: 1.5625;">Watch </span><span style="line-height: 18.0px;">the</span><span style="line-height: 1.5625;"> Duo Push Demo</span></a><span style="line-height: 1.5625;">\]</span>
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/5505155/5832709.png" class="confluence-embedded-image confluence-thumbnail" width="150" /></span>
+<span style="font-family: monospace;line-height: 1.4285715;">Photo
+credit:
+ </span><a href="https://www.duosecurity.com" class="external-link">Duo Security</a>
+
+For smartphone or tablet users (iPhone, Android, Blackberry, Windows
+Phone), the Duo Mobile app is available for free. A push notification
+will be sent to the device, and users can simply confirm the login with
+one tap.
+
+### Duo Mobile Passcodes
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/5505155/5832711.png" class="confluence-embedded-image confluence-thumbnail" height="250" /></span>
+
+`Photo credit: Duo Security`
+
+The Duo Mobile app can also be used to generate numeric passcodes, even
+when internet and cell service is unavailable. Press the key icon to
+generate a passcode. The passcode is then entered manually at the login
+prompt to complete authentication.
+
+### SMS Passcodes
+
+<span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/5505155/5832712.png" class="confluence-embedded-image confluence-thumbnail confluence-content-image-border" width="100" /></span>
+
+For non-smartphone users, Duo can send passcodes via normal text
+messages which are entered manually to complete login. Please note since
+this is an SMS message it may not be free, depending on the details of
+the particular cell phone plan.
+
+### <span style="color: rgb(0,0,0);font-size: 16.0px;line-height: 1.5625;">Phone Callback</span>
+
+For users with cell phones who prefer not to use any of the above
+methods and for those with landline phones, Duo will call the phone and
+provide a passcode via automatic voice message. The passcode is then
+entered manually to complete the login.
+
+### YubiKey <span style="color: rgb(61,61,61);font-size: 12.0px;line-height: 1.6666666;">\[</span><a href="http://www.yubico.com" class="external-link">Yubico</a><span style="color: rgb(61,61,61);font-size: 12.0px;line-height: 1.6666666;">\]</span>
+
+<span
+style="color: rgb(61,61,61);font-size: 12.0px;line-height: 1.6666666;"><span
+class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/5505155/5832710.jpg" class="confluence-embedded-image confluence-thumbnail" width="150" /></span>
+`Photo credit: Yubico`
+</span>
+
+YubiKeys are USB hardware tokens that generate passcodes when pressed.
+They appear as a USB keyboard to the computer they are connected to, and
+so require no driver software with almost all modern operating systems.
+YubiKeys are available from the Union Bookstore at UNL for a one-time
+cost of $25 each. Users may also purchase them directly from
+<a href="https://store.yubico.com" class="external-link">Yubico</a> if
+desired; this does require stopping by either HCC location in person to
+have the YubiKey added to the user's account. For your convenience, HCC
+often carries some YubiKeys as well; these may only be purchased via a
+Cost Object transfer.
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[duo-push.png](attachments/5505155/5832709.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[black\_single.jpg](attachments/5505155/5832710.jpg) (image/jpeg)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[duo-mobile-passcodes.png](attachments/5505155/30446716.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[2013-11-26 15.57.32.png](attachments/5505155/5832715.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
+Shot 2013-11-27 at 9.57.26 AM.png](attachments/5505155/5832713.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
+Shot 2013-11-27 at 9.58.00 AM.png](attachments/5505155/5832714.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[2013-11-26 15.57.32.png](attachments/5505155/5832712.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[2013-11-27 09.57.48.png](attachments/5505155/5832716.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[2013-11-27 09.59.23.png](attachments/5505155/5832717.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[duo-mobile-passcodes.png](attachments/5505155/5832711.png)
+(image/png)
+
+Document generated by Confluence on Oct 24, 2018 14:47
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/quickstarts/setting_up_gitlab_on_hcc_clusters.md b/content/quickstarts/setting_up_gitlab_on_hcc_clusters.md
new file mode 100644
index 00000000..2f39e6a0
--- /dev/null
+++ b/content/quickstarts/setting_up_gitlab_on_hcc_clusters.md
@@ -0,0 +1,114 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Quick Start Guides](Quick-Start-Guides_1245279.html)
+5. [Using UNL's GitLab instance](11304962.html)
+
+<span id="title-text"> HCC-DOCS : Setting up GitLab on HCC Clusters </span>
+===========================================================================
+
+Created by <span class="author"> Carrie Brown</span>, last modified on
+May 30, 2017
+
+The easiest way to use GitLab on HCC clusters is by adding SSH keys to
+your account.
+
+<span
+class="aui-icon aui-icon-small aui-iconfont-info confluence-information-macro-icon"></span>
+
+These steps must be repeated for each cluster that you wish to use the
+service on.
+
+After you have [setup your GitLab account](11304962.html), follow these
+steps to add SSH keys to your account:
+
+1. Login to the cluster that you wish to set up GitLab access on.
+
+2. Check for an existing key by typing the command:
+
+ ``` syntaxhighlighter-pre
+ cat ~/.ssh/id_rsa.pub
+ ```
+
+ If you see a long string of characters starting with \`ssh-rsa\`
+ then you can skip step 3 and proceed directly to step 4.
+
+3. Generate an SSH Key pair with the command below, replacing
+ **your\_email\_here** with the email you used to login to GitLab:
+
+ ``` syntaxhighlighter-pre
+ ssh-keygen -t rsa -C "your_email_here"
+ ```
+
+ This command will prompt you for a location and filename to store
+ the key pair and for a password. When prompted for the location and
+ filename, just press enter to use the default. If you use a
+ different name, the key will not be used automatically.
+
+ Note: It is a best practice to use a password for an SSH key, but it
+ is not required and you can skip creating a password by pressing
+ enter.
+
+ If you want to change the password of your key later, you can use
+ the following command:
+
+ ``` syntaxhighlighter-pre
+ ssh-keygen -p <keyname>
+ ```
+
+4. Retrieve your public key with the command:
+
+ ``` syntaxhighlighter-pre
+ cat ~/.ssh/id_rsa.pub
+ ```
+
+ Copy all the text after the command (starting with ssh-rsa) to but
+ not including the next prompt (ending with your email address).
+
+5. Add the public key to your GitLab account by navigating to your
+ Account Information screen. After logging in, click the arrow next
+ to your profile icon in the top right corner. Click on Profile
+ Settings.
+
+ <span
+ class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/18548049/18548051.png" class="confluence-embedded-image image-center" height="250" /></span>
+ Then click SSH Keys from the top menu.
+ <span
+ class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/18548049/18548052.png" class="confluence-embedded-image image-center" width="1100" /></span>
+
+ Paste your copied key into the Key box. The Title box will
+ automatically populate with your email. You can accept this title or
+ change it to a custom title of your choosing. We recommend adding
+ the cluster name to the title so you can easily identify what key is
+ associated with a particular machine.
+
+ <span
+ class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/18548049/18548053.png" class="confluence-embedded-image image-center" height="400" /></span>Click
+ the Add Key button to save the key to your account.
+
+Now you can clone and push repositories as usual. When pushing to an
+existing repository, you will be prompted for the passkey associated
+with the keys (if you added one).
+
+
+
+
+
+
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2017-5-30\_12-43-20.png](attachments/18548049/18548051.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2017-5-30\_12-46-11.png](attachments/18548049/18548052.png)
+(image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[image2017-5-30\_12-49-51.png](attachments/18548049/18548053.png)
+(image/png)
+
+Document generated by Confluence on Oct 24, 2018 14:47
+
+[Atlassian](http://www.atlassian.com/)
diff --git a/content/quickstarts/using_unl_gitlab_instance.md b/content/quickstarts/using_unl_gitlab_instance.md
new file mode 100644
index 00000000..3e86e241
--- /dev/null
+++ b/content/quickstarts/using_unl_gitlab_instance.md
@@ -0,0 +1,78 @@
+1. [HCC-DOCS](index.html)
+2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
+3. [HCC Documentation](HCC-Documentation_332651.html)
+4. [Quick Start Guides](Quick-Start-Guides_1245279.html)
+
+<span id="title-text"> HCC-DOCS : Using UNL's GitLab instance </span>
+=====================================================================
+
+Created by <span class="author"> Adam Caprez</span>, last modified by
+<span class="editor"> Carrie Brown</span> on May 30, 2017
+
+<a href="http://git-scm.com/" class="external-link">Git</a> is a free
+and open source distributed version control system designed to handle
+everything from small to very large projects with speed and efficiency.
+ Users are encouraged to make use of git for source code management of
+their projects.
+
+<a href="https://about.gitlab.com/" class="external-link">GitLab</a><span
+style="line-height: 1.4285715;"> </span><span
+style="line-height: 1.4285715;"> is a web-based Git repository manager
+with wiki and issue tracking features. UNL ITS hosts an instance of
+GitLab at
+</span><a href="https://git.unl.edu" class="external-link">git.unl.edu</a>,
+which can be accessed using credentials from any campus participating in
+the InCommon federation<span style="line-height: 1.4285715;">. This
+includes UNL, UNO, and UNMC, as well as most major US Universities.
+ Using a service such as GitLab provides several additional advantages
+over a </span>simple repository<span
+style="line-height: 1.4285715;"> including collaboration, repository
+management, issue tracking, and code review. </span>
+
+To get started, go
+to <a href="https://git.unl.edu" class="external-link">git.unl.edu</a>.
+ Click the "Sign in with Shibboleth" button.
+
+<span
+class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/11304962/11304982.png" class="confluence-embedded-image image-center" height="400" /></span>
+
+This will take you to the InCommon site to select your school,
+organization, etc. You may wish to choose the "Remember my selection
+permanently" option to bypass this step in the future.
+
+<span
+class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/11304962/11304983.png" class="confluence-embedded-image image-center" height="400" /></span>
+
+<span style="line-height: 1.4285715;">Next, scroll through to find your
+particular institution. For example, for UNL users, select "University
+of Nebraska-Lincoln".</span>
+
+<span
+class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/11304962/11304984.png" class="confluence-embedded-image image-center" height="400" /></span>
+
+After you click "Next", you will be redirected to your particular
+institution or campus's login page. Complete the login to proceed to
+your account's Dashboard page and begin using GitLab.
+
+For more information on using GitLab on the HCC Clusters, see [Setting
+up GitLab on HCC
+Clusters](Setting-up-GitLab-on-HCC-Clusters_18548049.html).
+
+See <a href="https://about.gitlab.com/2014/02/26/getting-started-with-gitlab/" class="external-link">Getting Started with Git and GitLab</a> or
+the full
+GitLab <a href="http://doc.gitlab.com/ce/" class="external-link">documentation</a> for
+additional help.
+
+Attachments:
+------------
+
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[signin\_1.png](attachments/11304962/11304982.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[signin\_2.png](attachments/11304962/11304983.png) (image/png)
+<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
+[signin\_3.png](attachments/11304962/11304984.png) (image/png)
+
+Document generated by Confluence on Oct 24, 2018 14:47
+
+[Atlassian](http://www.atlassian.com/)
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--
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