Verified Commit a0bf0276 authored by Adam Caprez's avatar Adam Caprez
Browse files

Fix references enough so the site will build.

parent 4a4df822
......@@ -51,7 +51,7 @@ Select the other options based on your computing needs. Note that a SLURM Job wi
Many popular `python` and `R` packages are already installed and available within Jupyter Notebooks.
However, it is possible to install custom packages to be used in notebooks by creating a custom Anaconda
Environment. Detailed information on how to create such an environment can be found at
[Using an Anaconda Environment in a Jupyter Notebook on Crane]({{< relref "using_anaconda_package_manager/#using-an-anaconda-environment-in-a-jupyter-notebook-on-crane" >}}).
[Using an Anaconda Environment in a Jupyter Notebook on Crane]({{< relref "/Applications/Using_Your_Own_Software/using_anaconda_package_manager#using-an-anaconda-environment-in-a-jupyter-notebook-on-crane" >}}).
---
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......@@ -4,7 +4,7 @@ description = "Example of how to profile BLAST using Allinea Performance Reports
+++
Simple example of using
[BLAST]({{< relref "/guides/running_applications/bioinformatics_tools/alignment_tools/blast/running_blast_alignment" >}}) 
[BLAST]({{< relref "/Applications/Application_Specific_Guides/bioinformatics_tools/alignment_tools/blast/running_blast_alignment" >}}) 
with Allinea Performance Reports (`perf-report`) on Crane is shown below:
{{% panel theme="info" header="blastn_perf_report.submit" %}}
......
......@@ -3,7 +3,7 @@ title = "Ray with Allinea Performance Reports"
description = "Example of how to profile Ray using Allinea Performance Reports"
+++
Simple example of using [Ray]({{< relref "/guides/running_applications/bioinformatics_tools/de_novo_assembly_tools/ray" >}})
Simple example of using [Ray]({{< relref "/Applications/Application_Specific_Guides/bioinformatics_tools/de_novo_assembly_tools/ray" >}})
with Allinea PerformanceReports (`perf-report`) on Tusker is shown below:
{{% panel theme="info" header="ray_perf_report.submit" %}}
......
......@@ -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 Crane. In order to use these resources, the ["biodata" module] ({{<relref "/guides/running_applications/bioinformatics_tools/biodata_module">}}) needs to be loaded first. The **$BLAST** variable contains the following currently available databases:
HCC hosts multiple BLAST databases and indices on Crane. In order to use these resources, the ["biodata" module] ({{<relref "/Applications/Application_Specific_Guides/bioinformatics_tools/biodata_module">}}) needs to be loaded first. The **$BLAST** variable contains the following currently available databases:
- **16SMicrobial**
- **env_nt**
......
......@@ -61,7 +61,7 @@ will keep running with the options defined in the initial
Simple example of using DMTCP with
[BLAST]({{< relref "/guides/running_applications/bioinformatics_tools/alignment_tools/blast/running_blast_alignment" >}})
[BLAST]({{< relref "/Applications/Application_Specific_Guides/bioinformatics_tools/alignment_tools/blast/running_blast_alignment" >}})
on crane is shown below:
{{% panel theme="info" header="dmtcp_blastx.submit" %}}
......
......@@ -59,7 +59,7 @@ 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]({{< relref "setting_up_and_using_duo">}})
section: [Setting up and using Duo]({{< relref "/Accounts/setting_up_and_using_duo">}})
**Important Notes**
......
......@@ -59,7 +59,7 @@ 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]({{< relref "setting_up_and_using_duo">}})
section: [Setting up and using Duo]({{< relref "/Accounts/setting_up_and_using_duo">}})
**Important Notes**
......
......@@ -36,7 +36,7 @@ how to install the necessary software for your operating system
Information on how to change or retrieve your password can be found on
the documentation page: [How to change your
password]({{< relref "how_to_change_your_password" >}})
password]({{< relref "/Accounts/how_to_change_your_password" >}})
All passwords must be at least 8 characters in length and must contain
......
......@@ -11,8 +11,7 @@ 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]({{< relref "/guides/running_applications/compiling_source_code" >}}).
Before writing a submit file, you may need to compile your application.
- [Ensure proper working directory for job output](#ensure-proper-working-directory-for-job-output)
- [Creating a SLURM Submit File](#creating-a-slurm-submit-file)
......
......@@ -34,7 +34,7 @@ automatically match the `ntasks-per-node` value (in this example 16).
Directions to compile OpenMP can be found on 
[Compiling an OpenMP Application]
({{< relref "/guides/running_applications/compiling_source_code/compiling_an_openmp_application" >}}).  
({{< relref "/Applications/Using_Your_Own_Software/compiling_an_openmp_application" >}}).  
### Further Documentation
......
......@@ -5,7 +5,7 @@ weight = "22"
+++
##### Use of Duo two-factor authentication is **required** to access HCC resources.
##### Please see [Setting up and Using Duo]({{< relref "setting_up_and_using_duo" >}}).
##### Please see [Setting up and Using Duo]({{< relref "/Accounts/setting_up_and_using_duo" >}}).
---
- [Access to HCC Supercomputers] (#access-to-hcc-supercomputers)
- [File Transferring with HCC Supercomputers] (#file-transfering)
......
......@@ -5,7 +5,7 @@ weight = "20"
+++
##### Use of Duo two-factor authentication is **required** to access HCC resources.
##### Please see [Setting up and Using Duo]({{< relref "setting_up_and_using_duo" >}}).
##### Please see [Setting up and Using Duo]({{< relref "/Accounts/setting_up_and_using_duo" >}}).
---
......
......@@ -5,7 +5,7 @@ weight = "22"
+++
##### Use of Duo two-factor authentication is **required** to access HCC resources.
##### Please see [Setting up and Using Duo]({{< relref "setting_up_and_using_duo" >}}).
##### Please see [Setting up and Using Duo]({{< relref "/Accounts/setting_up_and_using_duo" >}}).
---
This quick start will help you configure your MobaXterm installation to work with HCC resources.
......@@ -76,4 +76,4 @@ In the Generator window, click `Generate` and move your mouse around in the `Key
After the key is generated, go to the `Conversions` tab and select `Export OpenSSH key` and save it to your local machine.
{{< figure src="/images/moba/exportssh.png" height="450" >}}
**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.**
\ No newline at end of file
**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.**
......@@ -11,8 +11,7 @@ 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]({{< relref "/guides/running_applications/compiling_source_code" >}}).
Before writing a submit file, you may need to compile your application.
- [Ensure proper working directory for job output](#ensure-proper-working-directory-for-job-output)
- [Creating a SLURM Submit File](#creating-a-slurm-submit-file)
......
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