Bioconda is a distribution of bioinformatics software realized as a channel for the versatile Conda package manager. Key features of Conda are
- a command line client for simple installation and dependency handling in the spirit of
conda install mypackage,
- very easy package creation,
- a mechanism for creating isolated environments that allows different package versions to coexist.
These features turn Conda into the perfect package manager for bioinformatics, where analyses often involve the application of various tools with sometimes complicated and even conflicting dependencies or mixtures of different languages. Ultimately, the usage of Conda should help to perform reproducible science. Bioconda already contains over 1500 bioinformatics related packages.
Setup and usage¶
Linux (any distribution with GLIBC >=2.12) or Max OS.
Step 1: Install Conda¶
To use bioconda, you need to install the Conda package manager which is most easily obtained via the Miniconda Python distribution. Miniconda can be installed to your home directory without admin priviledges.
Step 2: Setup Bioconda¶
After installing Miniconda, you can use the
conda command to setup bioconda with:
conda config --add channels conda-forge conda config --add channels defaults conda config --add channels r conda config --add channels bioconda
r channel is added to satisfy the R language
dependencies of some packages as well as some non-R dependencies.
Even if you don’t plan on installing R packages, the r channel is required
for some Bioconda packages. Similarly, the
conda-forge channel contains
many dependencies that are not strictly for bioinformatics but that are
required for Bioconda packages to work (see more at
Be sure to add the channels in the given order, because it defines how conda handles ambiguity between channels.
See `http://conda.pydata.org/docs/channels.html`_ for more information.
Step 3: Install packages or create environments¶
Once the channels have been added, you can install packages, e.g.:
conda install bwa
Isolated environments (with e.g. specific software versions>`_ can be created via:
conda create -n myenviroment bwa=0.7.12
For more information, visit the Conda documentation or have a look at the command line options by executing:
Step 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.