_images/bioconda.png

Bioconda lets you install thousands of software packages related to biomedical research using the conda package manager.

NOTE: Bioconda supports only 64-bit Linux and macOS

Usage

First, install conda. Then perform a one-time set up of Bioconda with the following commands:

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict
What did these commands do?

In general, running conda config modifies your condarc file which can be found at ~/.condarc by default.

The first three commands add channels, from lowest to highest priority. The order is important to avoid problems with solving dependencies:

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

  • The defaults channel is the one set by default in a new installation of conda. It should be set to the lowest priority.

  • The bioconda channel enables installation of packages related to biomedical research.

  • The conda-forge channel (see docs) enables installation of general-purpose packages. Since bioconda heavily depends on the conda-forge channel, it is set to highest priority.

This command:

conda config --set channel_priority strict

avoids cryptic errors when tryng to install. It ensures that the channel priority configured above is respected when solving dependencies. See this section of the conda-forge docs for more info.

What if I don't want to modify my condarc?

Sometimes you might want to specify the channel priority directly in the conda command-line call when installing a package or creating an environment, and not edit the condarc file with the suggested conda config commands above.

In that case, you would need to add the following arguments to conda calls:

--channel conda-forge --channel bioconda --strict-channel-priority

For example, if you were creating an environment with bwa and samtools in it, you would use:

conda create -n myenv samtools bwa

–channel conda-forge –channel bioconda –channel defaults –strict-channel-priority

Note that conda interprets channels on the command line in order of decreasing priority (in contrast to conda config, where they are listed in increasing priority).

Now you can use conda to install and use any of the packages available in bioconda.

How do I speed up package installation?

Sometimes conda can spend a lot of time trying to solve dependencies for an environment. See How do I speed up package installation? in the FAQs for some options to improve this.

How do I get Docker containers of packages?

Every conda package in Bioconda has a corresponding Docker BioContainer automatically created and uploaded to Quay.io. A list of these and other containers can be found at the BioContainers Registry. For example:

docker pull quay.io/biocontainers/samtools:1.15.1--h1170115_0

If you have docker installed, you do not need any additional configuration.

Overview

The Bioconda channel is the primary output for users, but it takes a team of contributors and additional infrastructure to make it all happen. The entire system consists of the components illustrated in the diagram below.

_images/bioconda-dag.png

Legend (starting from the bottom):

① Over 1400 contributors who add, modify, update, and maintain recipes and packages

Details

Contributors to Bioconda add new recipes or update existing recipes by opening pull requests to GitHub. Contributors might include:

  • authors of the software

  • Bioconda core team

  • anyone interested creating a conda package

There’s even a Bioconda bot that watches common places for updates (like CRAN, PyPI, GitHub releases) and submits a pull request with the update for other contributors to review.

② A repository of recipes hosted on GitHub

Details

The full history of all recipes is stored in the repository of recipes on GitHub.

Contributors and Bioconda core team coordinate, collaborate, and help each other out via comments on GitHub in issues and pull requests which are tested (see ③). The goal is to get a working package that satisfies the Bioconda policies.

③ A build system that turns each recipes into a conda package and a Docker container

Details

Every time changes are pushed to a GitHub pull request (e.g., new recipe or updates to recipe), all of these changes are automatically built and tested. The results are reported back to the GitHub pull request page. Contributors work together to fix any issues (which are tested again) and the process repeats until all tests pass.

Our build system, bioconda-utils, orchestrates the various building and testing steps on Azure Pipelines. The output consists of both a conda package and a Biocontainer that can be inspected before merging the pull request.

④ A repository of packages and a registry of containers containing over 8000 bioinformatics packages

Details

When all tests pass and the pull request is merged into the main branch, two things happen:

  1. A final conda package is built and uploaded to the Bioconda channel on anaconda.org on anaconda.org.

  2. That same conda package is installed into a Docker container which is then uploaded to the Biocontainers registry.

⑤ Users can then use the package with conda install or docker pull

Details

See above for how to configure the conda channels. Using docker containers just needs docker installed.

Package downloads

The following plots show the recent usage of Bioconda in terms of number of downloads.

You can browse all packages in the Bioconda channel.

Acknowledgments

The Bioconda channel could not exist without support from:

  • Anaconda, Inc in the form of providing unlimited (in time and space) storage for packages in the channel.

  • Circle CI via an open source plan including free Linux and MacOS builds.

  • Amazon Web Services in the form of storage for BioContainers as well as compute credits.

  • Azure DevOps open source plan

  • GitHub Actions open source plan

The Bioconda logo is a derivative mark of Anaconda ®, a trademark of Anaconda, Inc registered in the U.S. and other countries. Anaconda, Inc. grants permission of the derivative use but is not associated with Bioconda.

Citing Bioconda

When using Bioconda please cite our article:

Grüning, Björn, Ryan Dale, Andreas Sjödin, Brad A. Chapman, Jillian Rowe, Christopher H. Tomkins-Tinch, Renan Valieris, the Bioconda Team, and Johannes Köster. 2018. Bioconda: Sustainable and Comprehensive Software Distribution for the Life Sciences. Nature Methods, 2018 doi:10.1038/s41592-018-0046-7.

Contributors

Core

Team

Bioconda would not exist without the continuous hard work and support of the wonderful community which includes over 1400 (as of 2022) contributors.

Table of contents