For reproducible data science, it is crucial that software libraries and tools are provided via an easy to use, unified interface, such that they can be easily deployed and sustainably managed. With its ability to maintain isolated software environments, the integration into major workflow management systems and the fact that no administration privileges are needed, the Conda package manager is the ideal tool to ensure sustainable and reproducible software management. With Bioconda, we unlock Conda for the life sciences. Bioconda offers a comprehensive resource of thousands of software libraries and tools that is maintained by hundreds of international contributors. Although it is among the youngest, it outperforms all competing projects by far in the number of available packages. With over six million downloads so far, Bioconda packages have been well received by the community. We invite everybody to join the Bioconda community, participate in maintaining or publishing new software, and reach the goal of a central, comprehensive, and language-agnostic collection of easily installable software for the life sciences.

Data and code availability

Data and code underlying the presented results are enclosed in a Snakemake workflow archive available at https://doi.org/10.5281/zenodo.1068297. The archive can also be used to automatically reproduce all results and figures presented in this work. Also see the "Life Sciences Reporting Summary".

Acknowledgments

We thank the participants of various hackathons (e.g., the GalaxyP and IUC contribution fest, ELIXIR BioContainers and NETTAB hackathon) and all contributors that joined us after writing this manuscript for porting numerous packages to Bioconda. We thank the Anaconda Inc. team and the conda-forge team for the excellent cooperation and support. The Bioconda project receives funding from Anaconda, Inc., Austin, TX, USA, in the form of unlimited (in time and space) storage for Bioconda packages on their hosting service (https://anaconda.org). Further, the project has been granted extended build times from Travis CI (https://travis-ci.com) and a free open source Linux and MacOS builds plan from Circle CI (https://circleci.com). The Bioconda community would like to thank ELIXIR (https://www.elixir-europe.org) for their constant support and donating staff. Ryan Dale was supported by the Intramural Program of the National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, USA. Johannes Köster was supported by the The Netherlands Organisation for Scientific Research (NWO) via a VENI grant and (in part) by German Research Foundation SFB 876.

Author contributions

Kyle Beauchamp, Christian Brueffer, Brad Chapman, Ryan Dale, Florian Eggenhofer, Björn Grüning, Johannes Köster, Elmar Pruesse, Martin Raden, Jillian Rowe, Devon Ryan, Ilya Shlyakter, Andreas Sjödin, Christopher Tomkins-Tinch, and Renan Valieris (in alphabetical order) have written the manuscript. Johannes Köster has drafted and finalized the manuscript. Johannes Köster and Ryan Dale have conducted the data analysis. Dan Ariel Søndergaard contributed by supervising student programmers on writing Conda package recipes and maintaining the connection with ELIXIR. All other authors have contributed or maintained recipes.

Competing Financial Interests

No competing interests.