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. OSX packages are built using the OSX build environment on Travis CI.

The steps below describe how to contribute a new package. The following prerequisites are assumed:

• The conda command line tool. This comes with the full Anaconda scientific Python stack installation, or the slimmed-down Miniconda. The Python 3 version is recommended.
• docker
• git

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. See our guidelines for best practices and examples.

Step 2: Test the recipe

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

conda build recipes/your_package

If the recipe has dependencies in the bioconda channel (this is often the case), you will need to add --channel bioconda to the command. If the recipe is an R package, you will also need to add --channel r. For example many Bioconductor packages will be built using:

conda build recipes/your_package --channel bioconda --channel r

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

See below for building on OSX.

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

Step 4:

If you want to promote the Bioconda installation of your package, we recommend to add the following badge to your homepage:

[![bioconda-badge](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square)](http://bioconda.github.io)

This will display as . For other styles, replace ?style=flat-square with ?style=flat or ?style=plastic.

Building packages for Mac OSX

By default, recipes will be built for both Linux and OSX (see "The bioconda build system" section below) upon submitting a pull request. Many recipes build cleanly on Linux but not on OSX. The easy fix is to explicitly skip the OSX build using a platform-specific selector on a line in the meta.yaml that skips the build, like this:

build:
  skip: True  # [osx]

A better fix is to figure out what needs to be changed for a build to work on OSX, and include those changes using platform-specific selectors. Such changes could include tweaks to the build script, applying patches, or using OS-specific installation methods. See graphviz, blast, and UCSC utils like ucsc-pslcdnafilter for examples of these methods.

To set up a local OSX machine for building and testing OSX recipes, run scripts/travis-setup.sh. Several commands in this script will prompt for sudo privileges, but the script itself should be run as a regular user. This script will set up a conda environment in /anaconda and install necessary prerequisites.

To test all OSX recipes (skipping those that defineskip: True #[osx]) use:

scripts/build-packages.py --repository .

Managing multiple versions of a package

If there is interest to keep multiple versions of a package or to explicitly build an older version of a package, you can store those versions in subdirectories of the corresponding recipe, e.g.:

java-jdk/
├── 7.0.91
│   ├── build.sh
│   └── meta.yaml
├── build.sh
└── meta.yaml

There should always be a primary in the root directory of a package that is updated when new releases are made.

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 bioconda/bioconda-builder .)

Then test a recipe with:

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

If you wish the open a bash shell in the Docker container for manual debugging:

docker run -i -t --entrypoint /bin/bash bioconda/bioconda-builder

The bioconda build system

This repository is set up on Travis CI such that on every pull request, the following steps are performed once within the Docker CentOS 5 container and once within the OSX build environment:

• find all recipes in the recipes dir
• filter out recipes that have already been uploaded to the bioconda channel
• parse the remaining recipes to recursively find dependencies
• topologically sort the recipes such that when they are built in order, dependency packages are built first
• build and test each recipe
• add the recipe to the "local" channel so that subsequent recipes in this build can use it as a dependency if needed

If all recipes build and test without error, the pull request can be merged with the master branch. Upon merging, Travis-CI will detect the merge and the same steps will be performed again. In addition, at the end of the build, all built packages will be uploaded to the bioconda channel. This means that as soon as the Travis-CI tests pass on the master branch, the packages are now publicly available to all users.

Dependencies

There is currently no mechanism to define, in the meta.yaml file, that a particular dependency should come from a particular channel. This means that a recipe must have its dependencies in one of the following:

• as-yet-unbuilt recipes in the repo included in the PR
• bioconda channel
• r channel
• default Anaconda channel

Otherwise, you will have to write the recipes for those dependencies and include them in the PR. conda skeleton is very useful for Python (PyPI), Perl (CPAN), and R (CRAN) packages. Another option is to use anaconda search -t conda <dependency name> to look for other packages built by others. Inspecting those recipes can give some clues into building a version of the dependency for bioconda.

Python versions

By default, Python recipes (those that have python listed as a dependency) must be successfully built and tested on Python 2.7, 3.4, and 3.5 in order to pass. However, many Python packages are not fully compatible across all Python versions. Use the preprocessing selectors in the meta.yaml file along with the build/skip entry to indicate that a recipe should be skipped.

For example, a recipe that only runs on Python 2.7 should include the following:

build:
  skip: True  # [not py27]

Or a package that only runs on Python 3.4 and 3.5:

build:
  skip: True # [py27]

Alternatively, for straightforward compatibility fixes you can apply a patch in the meta.yaml.

Creating Bioconductor recipes

See scripts/bioconductor/README.md for details on creating and updating Bioconductor recipes.

Creating and updating UCSC tools

See scripts/ucsc/README.md for details on creating and updating recipes for UCSC programs.