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 turning these recipes into conda packages

• a repository of packages containing over 6000 bioinformatics packages ready to use with conda install

• over 600 contributors and 500 members who add, modify, update and maintain the recipes

The conda package manager makes 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 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.

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.

Bioconda has been acknowledged by NATURE in their technology blog.

Each package added to Bioconda also 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.

Browse packages in the Bioconda channel: recipes

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Bioconda 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.

The Bioconda channel is sponsored by Anaconda, Inc in the form of providing unlimited (in time and space) storage. Bioconda is supported by Circle CI via an open source plan including free Linux and MacOS builds.

Using Bioconda

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.

See also

• 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, conda-forge is highest priority).

The conda-forge channel contains many general-purpose packages not already found in the defaults channel.

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

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

We invite all parties interested in adding/editing package recipes to join the bioconda team, so that their pull requests don’t require merging by the core team or other members. To do so, please fork our recipes have a read through the Conda documentation. If you ping @bioconda/core in a pull request we will review it and then add you to the team, if you desire.

5. Spread the word

Consider adding a badge to your posters and presentations to promote that a tool can be easily installed from Bioconda.

Contributors

Core

• Johannes Köster

• Ryan Dale

• Brad Chapman

• Chris Tomkins-Tinch

• Björn Grüning

• Andreas Sjödin

• Jillian Rowe

• Renan Valieris

• Marcel Bargull

• Devon Ryan

• Elmar Pruesse

Team

Bioconda has over 600 (as of 2019/1) contributors.

Contributor documentation

The rest of this documentation describes the build system architecture, the process of creating and testing recipes, and adding recipes to the bioconda channel.

Contents:

• Contributing
  • One-time setup
    • Git and GitHub (one-time setup)
    • Install the Circle CI client (optional)
    • Request to be added to the bioconda team (optional)
  • Contributing a recipe
    • 1. Update repo
    • 2. Write a recipe
    • 3. Test locally (optional)
    • 4. Push changes, wait for tests to pass, submit pull request
    • 6. Use your new recipe
  • Troubleshooting failed recipes
    • Reading bioconda-utils logs
    • HTTP 500 errors
    • HTTP 404 errors
    • ZLIB errors
    • /usr/bin/perl or /usr/bin/python not found
    • Troubleshooting failed mulled-build tests
    • Using the extended image
  • Build system
    • Stages of a bioconda build
    • The bulk branch
    • Labels
  • Guidelines for bioconda recipes
    • bioconda recipe checklist
    • Python
    • R (CRAN)
    • R (Bioconductor)
    • R (other sources)
    • Java
    • Perl
    • C/C++
    • Haskell
    • General command-line tools
    • Metapackages
    • Other examples of interest
    • Name collisions (identical names)
    • Tests
    • Link and unlink scripts (pre- and post- install hooks)
    • Versions
• Updating recipes
  • How it works
    • The components
    • Writing a filter
    • Writing a new hoster
• Updating recipes for a pinning change
• Linting
  • Skipping a lint check
    • Skipping persistently on a per-recipe basis
    • Skipping on a per-commit basis
  • Recipes duplicated in conda-forge
  • Description of Lint Checks
    • “in_other_channels”
    • “build_number_needs_bump”
    • “missing_home”
    • “missing_summary”
    • “missing_license”
    • “missing_tests”
    • “missing_hash”
    • “should_be_noarch”
    • “should_not_be_noarch_compiler”
    • “uses_git_url”
    • “uses_perl_threaded”
    • “uses_javajdk”
    • “uses_setuptools”
    • “has_windows_bat_file”
    • “setup_py_install_args”
    • “extra_identifiers_not_list”
    • “extra_identifiers_not_string”
    • “extra_identifiers_missing_colon”
    • “deprecated_numpy_spec”
    • “should_not_use_fn”
    • “should_use_compilers”
    • “compilers_must_be_in_build”
  • Developer docs
• FAQs
  • What’s the difference between Anaconda, conda, and Miniconda?
  • Recipe vs package
  • Continuous integration (Circle CI)
  • How is Circle CI set up and configured?
  • How are dependencies pinned to particular versions?
  • What’s the lifecycle of a bioconda package?
  • CircleCI macOS plans
  • Testing bioconda-utils locally
• Build system
  • Stages of a bioconda build
    • Configure the environment
  • The bulk branch
  • Labels
• Conda build v3
  • The new host section
  • Compiler tools
  • Global pinning
• Developer Docs
  • bioconda-utils
  • bioconda_utils
    • bot
    • lint
    • aiopipe
    • bioconductor_skeleton
    • build
    • circleci
    • cli
    • cran_skeleton
    • docker_utils
    • githandler
    • github_integration
    • githubhandler
    • gitter
    • graph
    • hosters
    • pkg_test
    • recipe
    • sphinxext
    • autobump
    • update_pinnings
    • upload
    • utils
  • bot
    • chat
    • commands
    • config
    • events
    • tasks
    • views
    • web
    • worker
  • lint
    • Writing additional checks
    • Module Autodocs