CONTRIBUTING.org

Subtrees

This repository includes the pipeline repositories as git subtrees. The following commands were used to add them:

for pipeline in bsseq rnaseq crispr scrnaseq; do
  git remote add $pipeline git@github.com:BIMSBbioinfo/pigx_$pipeline.git
  git subtree add --prefix=pipelines/$pipeline/ $pipeline master
done

for pipeline in chipseq sars-cov-2; do
  git remote add $pipeline git@github.com:BIMSBbioinfo/pigx_$pipeline.git
  git subtree add --prefix=pipelines/$pipeline/ $pipeline main
done

The common repository is included as a submodule by the pipelines. The submodules must be initialized.

git submodule update --init --checkout

To update all subtrees run:

for pipeline in bsseq rnaseq crispr scrnaseq; do
  git subtree pull --prefix=pipelines/$pipeline/ $pipeline master
done
for pipeline in chipseq sars-cov-2; do
  git subtree pull --prefix=pipelines/$pipeline/ $pipeline main
done

Website

The website is generated with the static site generator Haunt from the Scheme sources in the website directory. To publish the website, move the generated output to the root directory of the gh-pages branch and make a new commit.

Get the required dependencies with Guix:

guix environment --ad-hoc haunt guile guile-commonmark