Bioconda is a channel for the conda package manager specializing in bioinformatics software. Bioconda consists of:
- a repository of recipes hosted on GitHub
- a build system that turns these recipes into conda packages
- a repository of >1500 bioinformatics packages ready to use with
- Over 130 contributors that add, modify, update and maintain the recipes
Browse packages in the bioconda channel: Available packages
The conda package manager has recently made installing software a vastly more streamlined process. Conda is a combination of other package managers you may have encountered, such as pip, CPAN, CRAN, Bioconductor, apt-get, and homebrew. Conda is both language- and OS-agnostic, and can be used to install C/C++, Fortran, Go, R, Python, Java etc programs on Linux, Mac OSX, and Windows.
Conda allows separation of packages into separate repositories, or channels. The main defaults channel has a large number of common packages. Users can add additional channels from which to install software packages not available in the defaults channel. Bioconda is one such channel specializing in bioinformatics software.
bioconda supports only 64-bit Linux and Mac OSX.
1. Install conda¶
Bioconda requires the conda package manager to be installed. If you have an Anaconda Python installation, you already have it. Otherwise, the best way to install it is with the Miniconda package. The Python 3 version is recommended.
- What’s the difference between Anaconda, conda, and Miniconda?
- The conda FAQs explain how it’s easy to use with existing Python installations.
2. Set up channels¶
After installing conda you will need to add the bioconda channel as well as the other channels bioconda depends on. It is important to add them in this order so that the priority is set correctly (that is, bioconda is highest priority).
The conda-forge channel contains many general-purpose packages not already found in the defaults channel. The r channel contains common R packages used as dependencies for bioconda packages.
conda config --add channels conda-forge conda config --add channels defaults conda config --add channels r conda config --add channels bioconda
3. Install packages¶
Browse the packages to see what’s available.
bioconda is now enabled, so any packages on the bioconda channel can be installed into the current conda environment:
conda install bwa
Or a new environment can be created:
conda create -n aligners bwa bowtie hisat star
4. Join the team¶
Because our time is limited, the policy is to add a package if we need it ourselves. However, we invite anybody who wants to use Conda for bioinformatics to join the team and contribute new packages. To get started, have a look at our recipes and the Conda documentation. If you don’t want to join us permanently, you can also fork the recipes repository and create pull requests.
Bioconda has over 120 contributors, see here.
Bioconda is a derivative mark of Anaconda ®, a trademark of Continuum Analytics, Inc registered in the U.S. and other countries. Continuum Analytics, Inc. grants permission of the derivative use but is not associated with Bioconda.
The Bioconda channel is sponsored by Continuum Analytics.
The rest of this documentation describes the build system architecture, the process of creating and testing recipes, and adding recipes to the bioconda channel.
- Available packages
- One-time setup
- Contributing a recipe
- Troubleshooting failed recipes
- Build system
- Guidelines for