mkdocs.yml

site_name: Research Computing Documentation
repo_url: https://github.com/uabrc/uabrc.github.io/
edit_uri: blob/main/docs/

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  logo: images/logo.png

extra_css:
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copyright: Copyright &copy; 2021-2024 The University of Alabama at Birmingham.<br /><b>Still stuck after reading?</b> Email us at <a href="mailto:support@listserv.uab.edu" class="supportemail">support@listserv.uab.edu</a>

markdown_extensions:
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plugins: # order matters!
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        data_managment/transfer/globus.md: data_management/transfer/globus/index.md
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nav:
  - Home: index.md
  - News:
      - news/index.md
  - Account Management:
      - account/index.md
      - Research Computing System (RCS):
          - account/rcs/index.md
          - Create: account/rcs/create.md
          - Status: account/rcs/status.md
      - Code.rc (GitLab):
          - account/code.rc/index.md
          - Create: account/code.rc/create.md
          - Manage: account/code.rc/manage.md
      - External Collaborators:
          - account/xias/index.md
          - 1. Sponsor — Manage Sites: account/xias/1_sponsor_manage_sites.md
          - 2. Sponsor — Manage Users: account/xias/2_sponsor_manage_users.md
          - 3. Guests — Create XIAS Account: account/xias/3_guest_create_xias_account.md
          - 4. Guests — Create RCS Account: account/xias/4_guest_create_rcs_account.md
      - Your Responsibilities: account/responsibilities.md
      - Leaving UAB:
          - account/leaving/index.md
          - Continuing Collaboration: account/leaving/collaboration.md
          - Final Steps: account/leaving/final_steps.md
  - Data Management:
      - data_management/index.md
      - Storage:
          - data_management/storage/index.md
          - Cheaha Storage (GPFS):
              - data_management/storage/cheaha_storage_gpfs/index.md
              - User and Home Directories: data_management/storage/cheaha_storage_gpfs/individual_directories.md
              - Project Directories: data_management/storage/cheaha_storage_gpfs/project_directories.md
              - Network Scratch: data_management/storage/cheaha_storage_gpfs/network_scratch.md
              - Local Scratch: data_management/storage/cheaha_storage_gpfs/local_scratch.md
              - Temporary Files (/tmp/ Directory): data_management/storage/cheaha_storage_gpfs/temporary_files.md
          - Long Term Storage:
              - data_management/storage/lts/index.md
              - Tutorial:
                  - data_management/storage/lts/tutorial/index.md
                  - Individual LTS and s3cmd Workflow: data_management/storage/lts/tutorial/individual_lts_tutorial.md
                  - Shared LTS and s3cmd Workflow: data_management/storage/lts/tutorial/shared_lts_tutorial.md
              - Interfacing With LTS: data_management/storage/lts/interfaces.md
              - Identity and Access Management: data_management/storage/lts/iam_and_policies.md
              - UAB Core Accounts: data_management/storage/lts/lts_cores.md
              - FAQ: data_management/storage/lts/lts_faq.md
          - Code Storage: data_management/storage/code_storage.md
          - Storage Alternatives: data_management/storage/alternate_storage.md
      - Data Transfer Tools:
          - data_management/transfer/index.md
          - Globus:
              - data_management/transfer/globus/index.md
              - Getting Started: data_management/transfer/globus/login_to_globus.md
              - Install Globus Connect Personal: data_management/transfer/globus/gcp_install.md
              - Set Up Globus Connect Personal: data_management/transfer/globus/gcp_setup.md
              - Globus for Individuals: data_management/transfer/globus/globus_individual_tutorial.md
              - Globus for Organizations: data_management/transfer/globus/globus_organization_tutorial.md
              - Globus Group Management: data_management/transfer/globus/globus_group_management.md
          - RClone: data_management/transfer/rclone.md
          - FileZilla: data_management/transfer/filezilla.md
      - Research Data Responsibilities: data_management/research_data_responsibilities.md
  - Workflow Solutions:
      - Using the Shell: workflow_solutions/shell.md
      - Using Anaconda: workflow_solutions/using_anaconda.md
      - Using Workflow Managers: workflow_solutions/using_workflow_managers.md
      - Using Git: workflow_solutions/git.md
      - R Projects and Environments: workflow_solutions/r_environments.md
      - Software Containers: workflow_solutions/getting_containers.md
      - Software Collaboration With GitHub and GitLab: workflow_solutions/git_collaboration.md
      - Creating Sandbox Apps: workflow_solutions/creating_sandbox_apps.md
  - Cheaha Guide:
      - Getting Started: cheaha/getting_started.md
      - Tutorials:
          - cheaha/tutorial/index.md
          - Anaconda Environment Tutorial: cheaha/tutorial/pytorch_tensorflow.md
      - Cheaha Web Portal:
          - cheaha/open_ondemand/index.md
          - Using the Web Portal: cheaha/open_ondemand/ood_layout.md
          - HPC Desktop: cheaha/open_ondemand/hpc_desktop.md
          - Jupyter Notebook: cheaha/open_ondemand/ood_jupyter_notebook.md
          - JupyterLab: cheaha/open_ondemand/ood_jupyterlab.md
          - RStudio: cheaha/open_ondemand/ood_rstudio.md
          - MATLAB: cheaha/open_ondemand/ood_matlab.md
      - Hardware: cheaha/hardware.md
      - Software:
          - Pre-Installed Modules: cheaha/software/modules.md
          - Self-Installed Software: cheaha/software/software.md
      - Slurm:
          - Introduction: cheaha/slurm/introduction.md
          - Slurm Tutorial: cheaha/slurm/slurm_tutorial.md
          - Submitting Jobs: cheaha/slurm/submitting_jobs.md
          - Practical Batch Array Jobs: cheaha/slurm/practical_sbatch.md
          - Managing Jobs: cheaha/slurm/job_management.md
          - GPUs: cheaha/slurm/gpu.md
      - Job Efficiency: cheaha/job_efficiency.md
  - UAB Cloud (cloud.rc) Guide:
      - uab_cloud/index.md
      - Tutorial:
          - uab_cloud/tutorial/index.md
          - (1) Networks: uab_cloud/tutorial/networks.md
          - (2) Security Policies: uab_cloud/tutorial/security.md
          - (3) Instances: uab_cloud/tutorial/instances.md
          - (4) Volumes (Optional): uab_cloud/tutorial/volumes.md
      - Remote Access: uab_cloud/remote_access.md
      - Installing Software: uab_cloud/installing_software.md
      - Hardware: uab_cloud/hardware.md
      - Snapshots and Images: uab_cloud/snapshots.md
      - Sharing Cloud Environment: uab_cloud/sharing_cloud_environment.md
  - UAB Kubernetes Guide:
      - kubernetes/index.md
      - Startup: kubernetes/startup.md
      - Hardware: kubernetes/hardware.md
  - Code.rc (GitLab) Guide:
      - code.rc/index.md
  - National Research Computing Cyberinfrastructure:
      - national_ci/index.md
      - The Open Science Grid: national_ci/osg.md
      - NSF Cyberinfrastructure: national_ci/nsf_access.md
      - NIH Cyberinfrastructure: national_ci/nih.md
  - Grants & Contracts:
      - RC Facilities Description: grants/facilities.md
      - Acknowledging Us in Publications: grants/publications.md
      - Funding Opportunities: grants/opportunities.md
  - Outreach & Training:
      - Case Studies: education/case_studies.md
      - Research Computing Courses: education/courses.md
      - Training Resources: education/training_resources.md
      - Scientific Domain-Specific Analysis Software:
          - education/domain_specific_software/index.md
          - Genetics & Omics: education/domain_specific_software/omics.md
      - Research Operations Software: education/research_operations_software.md
      - Research Computing Days:
          - education/research_computing_days/index.md
  - Policies: policies.md
  - Reporting Documentation Errors: contributing/reporting_errors.md
  - Contributing Content: contributing/contributor_guide.md
  - Help:
      - help/index.md
      - Support: help/support.md
      - FAQ - Frequently Asked Questions: help/faq.md

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watch:
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