contributing-bioconda.qmd

# Contributing bioconda recipes

> Note that for simple updates, you can use the `bioconda-utils` tool to automate the process. Here I went through it more manually to understand the process better.

## Documentation

- Full documentation & workflow available [here](https://bioconda.github.io/contributor/index.html)

## Steps

- Forked and cloned locally: `gh repo clone MYUSER_NAME/bioconda-recipes`

- Added upstream remote (only needed once):
```
cd bioconda-recipes
git remote add upstream git@github.com:bioconda/bioconda-recipes.git
```

- Update local master branch from upstream (bioconda), and push to my fork (origin)

- Make a new branch

```
git checkout master
git pull upstream master
git push origin master
git checkout -b update_vg
```

- Edit the recipe file, e.g. for `vg`: `recipes/vg/meta.yaml`

- For this recipe, changes were:
	1. Updated version number from 1.56.0 to 1.59.0
	2. Calculate & update sha256 checksums (`sha256sum vg`)
	3. Linting changes (see below)

- Before submitting a PR, test locally with `bioconda-utils` (no need to do this really - will be done again on GitHub, just for practice)

- Used pixi to install: `pixi global install -c conda-forge -c bioconda bioconda-utils`

- Navigate to the `bioconda-recipes` directory and run:

```
bioconda-utils lint --git-range master
bioconda-utils build --docker --mulled-test --git-range master

# Note: master is correct here, as we are comparing our changes against the master branch
```

- After linting and building successfully...

- Add, commit, and push changes to fork

```
git add 
git commit -m "update vg to v1.59.0"
git push -u origin update_vg
```

- Make the PR on GitHub

- Once their checks are run and turn green, comment the following: `@BiocondaBot please add label`

- Once merged...

```
# Delete local branch
git branch -D my_branch

# Delete branch in GitHub fork
git push origin -d my_branch

# And keep on top of changes before next branch
git checkout master
git pull upstream master
```

- Wait for at least 30 minutes for changes to propagate to the bioconda channel