HowTos/mkdocs.yml at main · CCBR/HowTos · GitHub

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# Project Information
site_name: CCBR How Tos
site_author: Vishal Koparde, Ph.D., Samantha Sevilla, PhD.
site_description: >-
  Step-by-step detailed How To Guides for data management and other CCBR-relevant tasks.

# Repository
repo_name: CCBR/HowTos
repo_url: https://github.com/CCBR/HowTos
edit_uri: ""

# Copyright
copyright: Copyright &copy; 2025 CCBR

# Configuration
theme:
  name: readthedocs
  locale: en

# Plugins
plugins:
  - search
  - git-revision-date
  - minify:
      minify_html: true


# Customization
extra:
  generator: false
  social:
    - icon: fontawesome/solid/users
      link: https://ccbr.ccr.cancer.gov/
    - icon: fontawesome/brands/github
      link: https://github.com/CCBR
    - icon: fontawesome/solid/paper-plane
      link: mailto:vishal.koparde@nih.gov


# Extensions
markdown_extensions:
  - markdown.extensions.admonition
  - markdown.extensions.attr_list
  - markdown.extensions.def_list
  - markdown.extensions.footnotes
  - markdown.extensions.meta
  - markdown.extensions.toc:
      permalink: true
  - pymdownx.arithmatex:
      generic: true
  - pymdownx.caret
  - pymdownx.critic
  - pymdownx.details
  - pymdownx.highlight
  - pymdownx.inlinehilite
  - pymdownx.keys
  - pymdownx.mark
  - pymdownx.smartsymbols
  - pymdownx.snippets:
      check_paths: true
  - pymdownx.superfences
  - pymdownx.tabbed
  - pymdownx.tasklist:
      custom_checkbox: true
  - pymdownx.tilde

# Page Tree
nav:
  - Intro : index.md
  - GitHub:
    - Overview: GitHub/overview.md
    - Set-Up:
      - Preparing your environment: GitHub/howto_setup.md
      - Basic Commands: GitHub/howto_functions.md
    - Basics:
      - Creating your GitHub Repo: GitHub/basic_repo.md
      - Creating your Documentation: GitHub/basic_docs.md
      - Creating GitHub Actions: GitHub/basic_actions.md
      - Using Pre-Commit: GitHub/howto_precommit.md
    - Best Practices:
      - Projects,Pipelines: GitHub/sop_projpipes.md
      - TechDev: GitHub/sop_techdev.md
  - TechDev:
    - Best Practices: GitHub/sop_techdev.md
  - HPCDME :
    - Setup : HPCDME/setup.md
    - Biowulf2HPCDME: HPCDME/transfer.md
    - Helix2HPCDME: HPCDME/transferFromHelix.md
  - UCSC Tracks:
    - Overview: UCSC/overview.md
    - Creating Inputs: UCSC/creating_inputs.md
    - Creating Tracks Info: UCSC/creating_track_info.md
    - Creating Tracks: UCSC/creating_tracks.md
  - Creating an R Package:
    - Set-Up: Rpackage/setup.md
    - Creating the package: Rpackage/build_pkg.md
    - Troubleshooting: Rpackage/common_issues.md
  - Other How Tos:
      - Datashare: OtherHowTos/datashare.md
      - Zenodo: OtherHowTos/zenodo.md
      - LucidCharts: OtherHowTos/lucidcharts.md
  - Tutorials:
    - Snakemake: Tutorials/snakemake.md
  - Contributions: contributions.md