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mkdocs.yml
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mkdocs.yml
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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: https://github.com/CCBR/HowTos/edit/main/docs/
# Copyright
copyright: Copyright © 2022 CCBR
# Configuration
theme:
name: material
features:
- navigation.tabs
- navigation.top
- navigation.indexes
- toc.integrate
palette:
- scheme: default
primary: indigo
accent: indigo
toggle:
icon: material/toggle-switch-off-outline
name: Switch to dark mode
- scheme: slate
primary: red
accent: red
toggle:
icon: material/toggle-switch
name: Switch to light mode
logo: assets/images/doc-book.svg
favicon: assets/images/favicon.png
# 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:[email protected]
version:
provider: mike
# 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.betterem:
smart_enable: all
- pymdownx.caret
- pymdownx.critic
- pymdownx.details
- pymdownx.emoji:
emoji_index: !!python/name:material.extensions.emoji.twemoji
emoji_generator: !!python/name:material.extensions.emoji.to_svg
- pymdownx.highlight
- pymdownx.inlinehilite
- pymdownx.keys
- pymdownx.magiclink:
repo_url_shorthand: true
user: squidfunk
repo: mkdocs-material
- 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
- 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
- Tutorials:
- Snakemake: Tutorials/snakemake.md
- Contributions: contributions.md