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 7000 bioinformatics packages ready to use with conda install

• over 850 contributors and 570 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.

Browse packages in the Bioconda channel: Package Index

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.

News

• Nov 2019: Bioconda has been selected as one of 42 open source projects for being funded by the Chan Zuckerberg Initiative.

• Nov 2017: Bioconda has been acknowledged by NATURE in their technology blog.

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.

Acknowledgments

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.

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 850 (as of 2020/1) contributors.

Table of contents

• User Docs
  • Getting Started
    • 1. Install conda
    • 2. Set up channels
    • 3. Install packages
    • 4. Join the team
    • 5. Spread the word
  • Versions Supported in Bioconda
    • Operating Systems
    • Python
    • Unsupported versions
• Contributing to Bioconda
  • Initial Setup
    • 1. Create a Fork of our Recipes Repo
    • 2. Create Local “Clone”
    • 3. Continue with or without local builds
  • Contribution Workflow
    • 1. Create a Branch
    • 2. Make Some Edits
    • 3. Push Changes
    • 4. Create a Pull Request
    • 5. Delete your Branch
    • 6. Install Your Package
  • Testing Recipes Locally
    • Using the Circle CI Client
    • Using the “Bootstrap” Method
    • Using the “Debug” Method
  • Troubleshooting
    • 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
    • g++ or gcc not found
  • Build system
    • Stages of a bioconda build
      • Configure the environment
    • The bulk branch
    • Labels
  • Guidelines for bioconda recipes
    • bioconda recipe checklist
      • Stable urls
      • Hashes
      • Build numbers
      • .bat files
      • Comments in recipes
      • Filesystem Hierarchy Standard
      • Existing package exceptions
      • Packages appropriate for bioconda
      • “Noarch” packages
      • Dependencies
      • Patching
    • 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
  • Linting
    • Skipping a lint check
      • Skipping persistently on a per-recipe basis
      • Skipping on a per-commit basis
    • Lint Checks
      • Incomplete Recipe
        • “missing_home”
        • “missing_summary”
        • “missing_license”
        • “missing_tests”
        • “missing_hash”
        • “missing_version_or_name”
        • “empty_meta_yaml”
        • “missing_meta_yaml”
        • “missing_build”
        • “missing_build_number”
      • Noarch or not noarch
        • “should_be_noarch_python”
        • “should_be_noarch_generic”
        • “should_not_be_noarch_compiler”
        • “should_not_be_noarch_source”
        • “should_not_be_noarch_skip”
        • “should_not_use_skip_python”
      • Policy
        • “uses_vcs_url”
        • “folder_and_package_name_must_match”
        • “gpl_requires_license_distributed”
        • “should_not_use_fn”
        • “has_windows_bat_file”
        • “long_summary”
        • “cran_packages_to_conda_forge”
      • Syntax
        • “extra_identifiers_not_list”
        • “extra_identifiers_not_string”
        • “extra_identifiers_missing_colon”
        • “extra_skip_lints_not_list”
      • Recipe Parsing
        • “duplicate_key_in_meta_yaml”
        • “unknown_selector”
        • “conda_render_failure”
        • “jinja_render_failure”
        • “unknown_check”
      • Repository
        • “in_other_channels”
        • “build_number_needs_bump”
        • “build_number_needs_reset”
        • “recipe_is_blacklisted”
      • Deprecations
        • “uses_perl_threaded”
        • “uses_javajdk”
        • “deprecated_numpy_spec”
        • “uses_matplotlib”
      • Build helpers
        • “should_use_compilers”
        • “uses_setuptools”
        • “setup_py_install_args”
        • “compilers_must_be_in_build”
        • “cython_must_be_in_host”
        • “cython_needs_compiler”
      • Linter Errors
        • “linter_failure”
    • 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
    • Where can I find more info on meta.yaml?
  • Updating recipes
    • How it works
      • The components
      • Writing a filter
      • Writing a new hoster
  • Updating recipes for a pinning change
  • Conda build v3
    • The new host section
    • Compiler tools
    • Global pinning
• Developer Docs
  • bioconda-utils
  • Writing additional checks
  • Module Autodocs
  • Writing additional checks
  • Module Autodocs