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
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
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.
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 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.
Table of contents¶
- User Docs
- Contributing to Bioconda
- Initial Setup
- Contribution Workflow
- Testing Recipes Locally
- Build system
- Guidelines for
- bioconda recipe checklist
- R (CRAN)
- R (Bioconductor)
- R (other sources)
- General command-line tools
- Other examples of interest
- Name collisions (identical names)
- Link and unlink scripts (pre- and post- install hooks)
- Skipping a lint check
- Lint Checks
- Incomplete Recipe
- Noarch or not noarch
- Recipe Parsing
- Build helpers
- Linter Errors
- Developer docs
- 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
- Where can I find more info on
- Updating recipes
- Updating recipes for a pinning change
- Conda build v3
- Developer Docs