Packaging your bioinformatics tool with Bioconda and Galaxy

Saskia Hiltemann (Erasmus University, The Netherlands) and Eric Rasche (Freiburg University, Germany) have been invited by Melbourne Bioinformatics to run two Bioconda and Galaxy training events to help build Australia’s capability in computational biomedical research, and encourage contributions to these great community projects.

Conda is an open source package management system that makes bioinformatics software installation much easier and improves analysis reproducibility. By adding your own tool to the Bioconda ecosystem, it becomes widely available as an installable tool package for various operating systems and hardware that is stored in a fully-supported, global repository of bioinformatics tools.

Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biomedical research. There is a vibrant and active community of contributors around the world, and members of the Galaxy Training Network are responsible for generating, curating, and maintaining a large repository of Galaxy training materials that are freely accessible. The Galaxy project uses Conda to manage tool dependencies and installations, and many of the software packages in Bioconda have been wrapped by the Galaxy community.

This 2-day workshop will introduce participants to the features of Bioconda and Galaxy. The workshop is suited to someone who has made their own bioinformatics tool and would like to learn how to add it to the Bioconda repository.

Participants will be guided through the process of writing Bioconda recipes, and can expect to have written a recipe for their own tool at the completion of the workshop.

An introduction to Galaxy wrappers and the Galaxy Intergalactic Utilities Commision will include participants writing wrappers for their own tool.

Attendees will benefit most from this workshop if they have their own bioinformatics tool that they regularly use and extensive command line experience. Some provisions will be made for participants who do not have a current tool for working on, but intend to have one in the near future to add to Bioconda.

This is a hands-on workshop and attendees must bring their own laptops.