OpenTYNDP Custom Conda Recipes

Custom conda package recipes for the OpenTYNDP project, built and published to prefix.dev.

Repository Structure

.
├── .github/
│   └── workflows/
|       ├── build-and-upload.yml # CI/CD workflow for building and uploading
│       └── pr-build.yml         # CI/CD workflow for PR test builds
├── recipes/
│   └── snakemake/               # Custom snakemake build
│       └── meta.yaml
├── pixi.toml                    # Development environment configuration
└── README.md

Using Packages

Install packages from our custom channel:

# With pixi
pixi workspace channel add https://prefix.dev/open-tyndp 
pixi add "https://prefix.dev/open-tyndp::snakemake-minimal >=9"

# With conda/mamba
conda install -c https://prefix.dev/open-tyndp snakemake-minimal

Adding New Recipes

1. Create a new directory under recipes/ with your package name
2. Add a meta.yaml file following conda-build conventions
3. Create a PR - the workflow will automatically build and test
4. Once merged to main, packages are automatically uploaded to prefix.dev

From conda-forge or bioconda-recipes packages

1. Copy the directory containing the meta.yaml file for the targeted package from its conda-forge feedstock or the bioconda-recipes repository.

2. Add a local version identifier to the version, like 9.15.3+opentyndp or 9.15.3+opentyndp.1.

3. Update the source to something like:

   source:
     git_url: https://github.com/coroa/snakemake.git
     git_rev: v{{ version }}

4. Add setuptools-scm to the host requirements section

5. Create a PR to build and test

Local Development

Build recipes locally using pixi:

# Build a specific recipe
pixi run build recipes/snakemake

# Upload to channel (requires PREFIX_API_KEY)
pixi run upload

CI/CD Workflow

The repository uses GitHub Actions to:

• On Pull Requests: Build changed recipes and upload as artifacts for testing
• On Merge to Main: Build and upload packages to prefix.dev channel

Recipe Guidelines

• Use noarch: python or noarch: generic when possible for platform-independent packages
• Always include tests in meta.yaml
• Pin dependencies appropriately
• For git-based sources, add setuptools-scm to build dependencies if the package uses it

Example: Snakemake Custom Build

The recipes/snakemake directory contains a custom build of Snakemake from a specific git branch:

source:
  git_url: https://github.com/coroa/snakemake
  git_rev: fix/unstuck-windows

This allows us to test unreleased fixes before they're merged upstream.

License

Individual recipes may have different licenses. Check each recipe's meta.yaml for license information.