brentp/recipes

Conda recipes for the bioconda channel.

The bioconda channel

Conda is a platform and language independent package manager, that sports easy distribution, installation and version management of software. The bioconda channel is a Conda channel providing bioinformatics related packages. This repository hosts the corresponding recipes.

User guide

Please visit https://bioconda.github.io for details.

Developer guide

If you want to contribute new packages to Bioconda, you are invited to join the Bioconda team. Please post in the team thread on GitHub to ask for permission.

We build Linux packages inside a CentOS 5 docker container to maintain compatibility across multiple systems. The steps below describe how to contribute a new package. It is assumed you have docker and git installed.

Step 1: Create a new recipe

Fork this repository or create a new branch to work in. Within the new branch, create a recipe (your_package in this example) in the recipes directory.

Step 2: Test the recipe

When the recipe is ready first test it with your local conda installation via

conda build recipes/your_package

Then, you can test it in the docker container with:

docker run -v `pwd`:/bioconda-recipes bioconda/bioconda-builder --packages your_package

To optionally build for a specific Python version, provide the CONDA_PY environmental variable. For example, to build specifically for Python 3.4:

docker run -e CONDA_PY=34 -v `pwd`:/bioconda-recipes bioconda/bioconda-builder --packages your_package

To optionally build and test all packages (if they don't already exist), leave off the package name:

docker run -v `pwd`:/tmp/conda-recipes bioconda/bioconda-builder

If rebuilding a previously-built package and the version number hasn't changed, be sure to increment the build number in meta.yaml (the default build number is 0):

build:
  number: 1

Step 3: Submit a pull request

Once these local tests pass, submit a pull request to this repository. The travis-ci continuous integration service will automatically test the pull request.

When the PR tests pass, the PR can be merged into the master branch.

Travis-CI will again run tests. However, when testing the master branch, new, successfully-built packages will be uploaded to the bioconda conda channel. Once these tests pass, your new package can now be installed from anywhere using:

conda install -c bioconda your_package

Building packages for Mac OSX

If you want your package to be built for Mac OSX as well, you have to add it to the osx-whitelist.txt file in the root of this repository.

###Other notes

We use a pre-built CentOS 5 image with compilers installed as part of the standard build. To build this yourself, you can do:

docker login
cd scripts && docker build -t bicoonda/bioconda-builder .

###Creating Bioconductor recipes A helper script is provided for generating a skeleton recipe for Bioconductor packages. The scripts/bioconductor-scraper.py script accepts the name of a Bioconductor package (e.g., "Biobase"). This script:

• parses the Bioconductor web page for the tarball
• downloads the tarball to a temp file and extracts the DESCRIPTION file
• parses the DESCRIPTION file to identify dependencies
• converts dependencies to package names more friendly to conda, specifically prefixing bioconductor- or r- as needed and using lowercase package names
• writes a meta.yaml and build.sh file to recipes/<new package name>.

That is,

 scripts/bioconductor-scraper.py Biobase

results in the files:

recipes/bioconductor-biobase/meta.yaml
recipes/bioconductor-biobase/build.sh

After the recipe has been created, you can follow the build test instructions above.