Merge branch 'master' into '2012attachments'

# Conflicts: # content/events/2012/nebraska_supercomputing_symposium_12.md # content/events/2012/supercomputing_mini_workshop_2012.md

Merge branch 'master' into '2012attachments'
8c35f368 · Carrie A Brown · d7b6b0a0 · b595514a · 8c35f368 · 8c35f368
Commit 8c35f368 authored 6 years ago by Carrie A Brown
--- a/content/events/2012/supercomputing_mini_workshop_2012.md
+++ b/content/events/2012/supercomputing_mini_workshop_2012.md
@@ -3,6 +3,11 @@ title = "Supercomputing Mini Workshop 2012"
 description = "Supercomputing Mini Workshop 2012."
 +++

+Quick Link: <a href="http://go.unl.edu/supercomputing_mini_2012">http://go.unl.edu/supercomputing_mini_2012</a>
+
+Presentation
+============
+
 [Workshop Presentation](https://unl.box.com/s/qr0p96va5qrkhvvq8lcyvqnzfrz1q2c0)

 Submit files, code source files, and example scripts can be found in

--- a/content/events/2013/hcc_matlab_workshop_2013.md
+++ b/content/events/2013/hcc_matlab_workshop_2013.md
@@ -3,98 +3,27 @@ title = "HCC Matlab Workshop 2013"
 description = "HCC Matlab Workshop 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
-&lt;[matlab\_workshop.pdf](attachments/2851357/3178542.pdf)&gt;
-
-Time
-
-Title
-
-Description
-
-UNMC
-
-10am - 11am
-
-Demo/Hand-On Practice
-
-Implementing a MATLAB code on HCC supercomputers
-
-11am - 12pm
+&lt;[matlab\_workshop.pdf](https://unl.box.com/s/lulbnbrnr7xqwufrx5s20gxnyxpykn7j)&gt;

-Individual Consultation
+| 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     |

-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)
+-   Get started with [For Windows Users](https://hcc.unl.edu/docs/quickstarts/connecting/for_windows_users/)
+    or [For Mac/Linux Users](https://hcc.unl.edu/docs/quickstarts/connecting/for_maclinux_users/).
+-   Hands On: [MATLAB on HCC](https://hcc.unl.edu/docs/guides/submitting_jobs/submitting_matlab_jobs/)
 -   Sample code for MATLAB on HCC:
-    &lt;[matlab\_dir.zip](attachments/2851357/3178543.zip)&gt;
+    &lt;[matlab\_dir.zip](https://unl.box.com/s/u19fy7cjeswfl1wi7h1nkeeie8gl3z90)&gt;
 -   Sample code for Parallel MATLAB Job:
-    &lt;[parallel\_matlab\_dir.zip](attachments/2851357/3178544.zip)&gt;
-
-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)  
-
-
+    &lt;[parallel\_matlab\_dir.zip](https://unl.box.com/s/fhl3kf6hg8dmtozkphq3u2r58yexrppe)&gt;
--- a/content/events/2013/hcc_mpi_workshop_2013.md
+++ b/content/events/2013/hcc_mpi_workshop_2013.md
@@ -3,18 +3,7 @@ title = "HCC MPI Workshop 2013"
 description = "HCC MPI Workshop 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
-&lt;[mpi\_workshop.pdf](attachments/2851569/3178561.pdf)&gt;
+Workshop presentation slides &lt;[mpi\_workshop.pdf](https://unl.app.box.com/file/438884023344)&gt;

 | Time    | Title                   | Description                                    |
 |---------|-------------------------|------------------------------------------------|
@@ -25,23 +14,13 @@ 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).
+    Users](https://hcc.unl.edu/docs/quickstarts/connecting/for_windows_users/) or [For Mac/Linux
+    Users](https://hcc.unl.edu/docs/quickstarts/connecting/for_maclinux_users/).
 -   Sample code for Fortran/C on HCC:
-    &lt;[serial\_dir.zip](attachments/2851569/3178562.zip)&gt;
+    &lt;[serial\_dir.zip](https://unl.app.box.com/file/438858401843)&gt;
 -   Sample code for MPI on HCC:
-    &lt;[mpi\_dir.zip](attachments/2851569/3178563.zip)&gt;
+    &lt;[mpi\_dir.zip](https://unl.app.box.com/file/438885605405)&gt;
 -   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)  
+    HCC](https://hcc.unl.edu/docs/guides/submitting_jobs/submitting_an_mpi_job/).  


--- a/content/events/2013/june_2013_osg_workshop.md
+++ b/content/events/2013/june_2013_osg_workshop.md
@@ -3,11 +3,7 @@ title = "HCC OSG Workshop, June 2013"
 description = "HCC OSG Workstop, June 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>
+Location: Unity Room/212 in the Jackie Gaughan Multicultural Center

 | Time    | Title                                                 | Description                                                      |
 |---------|-------------------------------------------------------|------------------------------------------------------------------|

--- a/content/events/2013/supercomputing_mini_workshop_february_27_2013.md
+++ b/content/events/2013/supercomputing_mini_workshop_february_27_2013.md
@@ -15,16 +15,6 @@ 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
@@ -36,7 +26,7 @@ ssh tusker.unl.edu -l demoXXXX
 Preparation
 -----------

-**[Download](attachments/1246451/1179891.zip) the demo code.**
+**[Download](https://unl.box.com/s/kopsfrp6ibnfds65it0g2oe3zmp3jxtx) the demo code.**

 Copy the two folders to the clipboard 


--- a/content/faq/_index.md
+++ b/content/faq/_index.md
@@ -173,5 +173,5 @@ Of course! We have an open door policy and invite you to stop by
 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 (http://hcc.unl.edu/contact-us). 
+time to meet:  [Contact Us](https://hcc.unl.edu/contact-us).

--- a/content/guides/running_applications/Jupyter.md
+++ b/content/guides/running_applications/Jupyter.md
@@ -24,9 +24,8 @@ weight = 20

 	{{< figure src="/images/jupyterPush.png" >}}  

-3.	Choose a job profile. Select "Local Jupyter Notebook" for light tasks such as debugging or small-scale testing.
-Select the other options based on your computing needs. Note that a local Jupyter Notebook will save to your "home" 
-directory, while the other options save to your "work" directory.
+3.	Choose a job profile. Select "Noteboook via SLURM Job | Small (1 core, 4GB RAM, 8 hours)" for light tasks such as debugging or small-scale testing.
+Select the other options based on your computing needs. Note that a SLURM Job will save to your "work" directory.

 {{< figure src="/images/jupyterjob.png" >}}


--- a/content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/_index.md
+++ b/content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/_index.md
@@ -7,7 +7,7 @@ weight = "52"

 [BLAST] (https://blast.ncbi.nlm.nih.gov/Blast.cgi) 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) and [Running BLAST Alignment](running_blast_alignment) describe how to run some of the most common BLAST executables as a single job using the SLURM scheduler on HCC.
+The following pages, [Create Local BLAST Database]({{<relref "create_local_blast_database" >}}) and [Running BLAST Alignment]({{<relref "running_blast_alignment" >}}) describe how to run some of the most common BLAST executables as a single job using the SLURM scheduler on HCC.


 ### Useful Information

--- 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
@@ -28,7 +28,7 @@ $ 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] (../../../biodata_module) needs to be loaded first. The **$BLAST** variable contains the following currently available databases:
+HCC hosts multiple BLAST databases and indices on both Tusker and Crane. In order to use these resources, the ["biodata" module] ({{<relref "/guides/running_applications/bioinformatics_tools/biodata_module">}}) needs to be loaded first. The **$BLAST** variable contains the following currently available databases:

 - **16SMicrobial**
 - **env_nt**
@@ -50,12 +50,13 @@ HCC hosts multiple BLAST databases and indices on both Tusker and Crane. In orde
 - **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).
+If you want to create and use a BLAST database that is not mentioned above, check [Create Local BLAST Database]({{<relref "create_local_blast_database" >}}).


 Basic SLURM example of nucleotide BLAST run against the non-redundant **nt** BLAST database 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 of 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.
 {{% notice info %}}
 **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.**
+**This example will first copy your database to faster local storage called “scratch”.  This can greatly improve performance!**
 {{% /notice %}}

 {{% panel header="`blastn_alignment.submit`"%}}
@@ -95,6 +96,7 @@ The default BLAST output is in pairwise format. However, BLAST’s parameter **-
 Basic SLURM example of protein BLAST run against the non-redundant **nr **BLAST database with tabular output format and `8 CPUs` is shown below. Similarly as before, 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.
 {{% notice info %}}
 **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.**
+**This example will first copy your database to faster local storage called “scratch”.  This can greatly improve performance!**
 {{% /notice %}}

 {{% panel header="`blastx_alignment.submit`"%}}

--- a/content/guides/running_applications/bioinformatics_tools/alignment_tools/bwa/_index.md
+++ b/content/guides/running_applications/bioinformatics_tools/alignment_tools/bwa/_index.md
@@ -36,4 +36,4 @@ $  bwa COMMAND
 or check the [BWA manual] (http://bio-bwa.sourceforge.net/bwa.shtml).


-The page[Running BWA Commands](running_bwa_commands) shows how to run BWA on HCC.
+The page [Running BWA Commands]({{<relref "running_bwa_commands" >}}) shows how to run BWA on HCC.
--- a/content/guides/running_applications/bioinformatics_tools/alignment_tools/tophat_tophat2.md
+++ b/content/guides/running_applications/bioinformatics_tools/alignment_tools/tophat_tophat2.md
@@ -14,7 +14,7 @@ The basic usage of TopHat2 is:
 {{< highlight bash >}}
 $ [tophat|tophat2] [options] index_prefix [input_reads_pair_1.[fasta|fastq] input_reads_pair_2.[fasta|fastq] | input_reads.[fasta|fastq]]
 {{< /highlight >}}
-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)/[Bowtie2](bowtie2). 
+where **index_prefix** is the basename of the genome index to be searched. This index is generated prior running TopHat/TopHat2 by using [Bowtie]({{<relref "bowtie" >}})/[Bowtie2]({{<relref "bowtie2" >}}). 

 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.


--- a/content/guides/running_applications/bioinformatics_tools/biodata_module/_index.md
+++ b/content/guides/running_applications/bioinformatics_tools/biodata_module/_index.md
@@ -80,4 +80,4 @@ cp /scratch/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:  
-[Organisms](#organisms)
+[Organisms]({{<relref "organisms" >}})
--- 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
@@ -36,4 +36,4 @@ $ bamtools help COMMAND
 or check the BamTools web, https://github.com/pezmaster31/bamtools/wiki.


-The page [Running BamTools Commands](running_bamtools_commands) shows how to run BamTools on HCC.
+The page [Running BamTools Commands]({{<relref "running_bamtools_commands" >}}) shows how to run BamTools on HCC.
--- 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
@@ -42,4 +42,4 @@ $ samtools COMMAND
 or check the [SAMtools manual] (http://www.htslib.org/doc/samtools.html).


-The page [Running SAMtools Commands](running_samtools_commands) shows how to run SAMtools on HCC.
+The page [Running SAMtools Commands]({{<relref "running_samtools_commands" >}}) shows how to run SAMtools on HCC.
--- a/static/images/jupyterjob.png
+++ b/static/images/jupyterjob.png