Lab Conda Recipes

This repository contains custom conda package recipes for lab-maintained software and tools needed for our benchmarks, built using rattler-build and published to prefix.dev.

Overview

This is a monorepo containing multiple conda recipe feedstocks for packages that are either:

• Not yet available in conda-forge
• Require custom builds or patches for lab-specific use cases
• Experimental or in-development tools

Platform Support

Packages are built for multiple platforms:

Platform	Target	Status
Linux (x86_64)	linux-64	✅ Fully supported
macOS (Intel)	osx-64	✅ Fully supported
macOS (Apple Silicon)	osx-arm64	✅ Fully supported
Windows (x86_64)	win-64	✅ Fully supported

Noarch packages (pure Python/R without compiled code) are built once and work on all platforms. Platform-specific packages (with C/C++/Rust code) are built separately for each platform.

See docs/PLATFORM_SUPPORT.md for details on multi-platform builds.

Repository Structure

packages/
├── recipes/
│   ├── package-name-1/
│   │   ├── recipe.yaml
│   │   └── build.sh (optional)
│   ├── package-name-2/
│   │   ├── recipe.yaml
│   │   └── patches/ (optional)
│   └── ...
├── .github/
│   └── workflows/
│       ├── build.yml
│       └── pr-check.yml
└── README.md

Prerequisites

Installing rattler-build

# Using pixi (recommended)
pixi global install rattler-build

# Or using conda/mamba
conda install -c conda-forge rattler-build

# Or using cargo
cargo install rattler-build

Setting up prefix.dev authentication

For CI/CD (GitHub Actions) - Trusted Publishers:

This repository uses Trusted Publishers for secure, keyless authentication to prefix.dev:

1. Go to prefix.dev and navigate to the almost-conductor channel
2. Go to Settings > Trusted Publishers
3. Add your GitHub repository as a trusted publisher:
   • Repository owner: your-username-or-org
   • Repository name: your-repo-name
   • Workflow: .github/workflows/build.yml
4. Save - No API keys needed!

For local manual uploads (optional):

If you need to upload packages manually:

1. Generate an API token from prefix.dev Settings > Access Tokens
2. Set it as an environment variable:

   export PREFIX_API_KEY=your-token-here

Creating a New Recipe

1. Create recipe directory

mkdir -p recipes/your-package-name
cd recipes/your-package-name

2. Create recipe.yaml

The recipe.yaml file uses the rattler-build format (similar to conda-build but more modern):

context:
  name: your-package-name
  version: "1.0.0"

package:
  name: ${{ name }}
  version: ${{ version }}

source:
  url: https://github.com/org/repo/archive/v${{ version }}.tar.gz
  sha256: <sha256-hash>

build:
  number: 0
  noarch: generic  # Add this for platform-independent packages
  script:
    - cargo build --release  # or appropriate build command
    - mkdir -p $PREFIX/bin
    - cp target/release/binary $PREFIX/bin/

requirements:
  build:
    - ${{ compiler('c') }}
    - ${{ compiler('rust') }}
  host:
    - openssl
  run:
    - openssl

tests:
  - script:
    - your-package-name --version
    - your-package-name --help

about:
  homepage: https://github.com/org/repo
  license: MIT
  license_file: LICENSE
  summary: A brief description of your package
  description: |
    A longer description of what your package does
    and why it's useful.

3. Build locally

# From the recipe directory
rattler-build build --recipe recipe.yaml

# Or from repository root
rattler-build build --recipe recipes/your-package-name/recipe.yaml

4. Test the build

# Install the built package locally
pixi global install ./output/your-package-name-1.0.0-*.conda

# Or with conda/mamba
conda install -c ./output your-package-name

Contributing Guidelines

Submitting a new recipe

1. Fork and clone this repository
2. Create a new branch for your recipe:

   git checkout -b add-package-name

3. Add your recipe in recipes/package-name/
4. Test locally with rattler-build build
5. Commit and push:

   git add recipes/package-name/
   git commit -m "Add recipe for package-name v1.0.0"
   git push origin add-package-name

6. Open a Pull Request with:
   • Description of the package
   • Why it's needed for lab work
   • Build test results
   • Any special considerations

Updating an existing recipe

1. Update the version in recipe.yaml
2. Update checksums if source URL changed
3. Increment build number if version stays the same
4. Test the build locally
5. Submit PR with changelog notes

Recipe Best Practices

• Pin dependencies appropriately: Use version constraints that work but aren't overly restrictive
• Test thoroughly: Include meaningful tests in the tests section
• Document patches: If applying patches, document why in comments
• Keep it reproducible: Ensure builds are deterministic
• Use selectors wisely: For platform-specific requirements, use selectors like [linux], [osx], [win]
• Use noarch when possible: For pure Python/R packages, use noarch: python or noarch: generic to build once for all platforms

CI/CD Pipeline

This repository uses GitHub Actions to:

• Validate recipes on pull requests
• Build packages automatically on merge to main
• Upload to prefix.dev channel
• Test packages in clean environments

Publishing to prefix.dev

Packages are automatically published to the almost-conductor channel on prefix.dev when merged to the main branch.

To use packages from our channel:

# Add channel to your environment
pixi project channel add https://prefix.dev/almost-conductor

# Or with conda/mamba
conda config --add channels https://prefix.dev/almost-conductor

# Install a package
pixi add -c https://prefix.dev/almost-conductor r-anndata

Manual uploads (rarely needed, CI handles this automatically):

# Set your API token
export PREFIX_API_KEY=your-token-here

# Upload package
rattler-build upload prefix -c almost-conductor output/noarch/your-package-*.conda

Troubleshooting

Common Issues

Build fails with missing dependencies:

• Ensure all build/host/run requirements are specified
• Check that dependencies are available in conda-forge or our channel

SHA256 mismatch:

• Re-download the source and compute the hash:

  curl -sL <url> | sha256sum

Package not found after build:

• Check the output directory: ./output/
• Verify the package name and version match expectations

Upload fails:

• Verify trusted publisher is configured correctly on prefix.dev
• Check that repository owner/name matches exactly
• Ensure you have write access to the almost-conductor channel

Resources

• rattler-build documentation
• prefix.dev documentation
• conda-forge recipes (for examples)
• Recipe format reference
• Multi-platform builds (Linux, macOS, Windows support)

Maintainers

This repository is maintained by the lab team. For questions or issues:

• Open an issue in this repository
• Contact the lab bioinformatics team
• Check our internal documentation wiki

License

Individual recipes may have different licenses. Refer to each recipe's about.license field. This repository structure and tooling is provided as-is for lab use.