CIDC Bioinformatics Group Pipeline documentation

computation_wiki

This is the computation wiki for the CIDC-bioinformatics team.

We document how to run WES, RNA-seq, and ATAC-seq pipelines on google cloud, and many others at this central place.

All the documentations are written in plain markdown and deployed using the awesome MkDocs. The deployed website can be found at https://cimac-cidc.github.io/CIDC-bioinformatics-computation-wiki/

How to contribute

Please read Github flow for how a general workflow is executed.

This site collects the documentations for running RIMA, CHIPS, WES and TCR

How to contribute

1. Fork the GitHub repo:https://github.com/CIMAC-CIDC/CIDC-bioinformatics-computation-wiki

2. Git clone your fork.

3. Under ~/CIDC-bioinformatics-computation-wiki/docs, add markdown file in the corresponding sub-dir.

4. Edit ~/CIDC-bioinformatics-computation-wiki/mkdocs.yml to point the path to the newly added documentations.

5. Commit your changes, git push and do the pull request.

git status

git add *

git commit -m "what you've done"

git push origin master

Log

pip install mkdocs

##### Theme #####
## https://squidfunk.github.io/mkdocs-material/
pip install mkdocs-material

#### Extensions ####
### pymdown-extensions ###
## requirements
pip install markdown
pip install pygments
pip install fontawesome_markdown
## install
pip install pymdown-extensions

#### Plugins ####
pip install mkdocs-git-revision-date-plugin
pip install mkdocs-git-revision-date-localized-plugin
pip install mkdocs-minify-plugin