Fix references enough so the site will build.

content/Applications/Application_Specific_Guides/Jupyter.md

@@ -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" >}}).
 
 ---
 

content/Applications/Application_Specific_Guides/allinea_profiling_and_debugging/allinea_performance_reports/blast_with_allinea_performance_reports.md

@@ -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" %}}

content/Applications/Application_Specific_Guides/allinea_profiling_and_debugging/allinea_performance_reports/ray_with_allinea_performance_reports.md

@@ -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" %}}

content/Applications/Application_Specific_Guides/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 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**

content/Applications/Application_Specific_Guides/dmtcp_checkpointing.md

@@ -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" %}}

content/_index.md

@@ -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**
 

content/connecting/_index.md

@@ -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**
 

content/faq/_index.md

@@ -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

content/guides/submitting_jobs/_index.md

@@ -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)

content/guides/submitting_jobs/submitting_an_openmp_job.md

@@ -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
 

content/quickstarts/connecting/for_maclinux_users.md

@@ -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)

content/quickstarts/connecting/for_windows_users.md

@@ -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" >}}).
 ---
 
 

content/quickstarts/connecting/mobaxterm_windows.md

@@ -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.**

content/quickstarts/submitting_jobs.md

@@ -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)