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The 2017 Galaxy Community Conference (GCC2017) is being held in Montpellier, France, 26-30 June.  GCC2017 will include keynotes and accepted talks, poster sessions, demos, birds-of-a-feather meetups, exhibitors, and plenty of networking opportunities. There will also be three days of pre-conference activities, including hackathons and training. If you work in data-intensive biomedical research, there is no better place than GCC2017 to present your work and to learn from others.
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Thursday, June 29 • 10:00 - 10:20
Bioconda and BioContainers - Enabling Universal Reproducibility in Galaxy

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John Chilton, Department of Biochemistry and Molecular Biology, Penn State University
Marius Van den Beek, Institut Curie
Björn Grüning, Uni-Freiburg (ALU)
Galaxy Team   

Reproducible data analysis requires reproducible software installation. There are many approaches to reproducible software installation – DebianMed, Docker, homebrew-science, software modules, and others. Many work well in cloud and container-enabled environments – where the researcher has full control of a virtual machine or container host and may choose whatever software installation mechanism makes sense. However, these same approaches are less appropriate at high performance computing (HPC) centers where large centralized resources mean such freedom is unavailable. On the other hand, the HPC-centric approaches do not provide options such as ready-to-run software containers ideal for the cloud. Furthermore, some approaches are built to work with command-line scripting while others are built for specific computational platforms or deployment technologies. Here we will outline an approach that covers all of these scenarios with a great deal of flexibility – allowing for the execution of the same binaries regardless of which technologies are selected. For Galaxy in particular, this approach allows the same packages and binaries to be used inside and outside of containerized environments automatically without extra annotation in Galaxy tools.

This approach to reproducibility is the combination of Bioconda and BioContainers.We will update the community on progress in Bioconda adoption and demonstrate that it has improved Galaxy dependency management for both developers and deployers. We will then focus in depth on BioContainers - containerized environments built automatically from Bioconda packages and how they enable containerized tool execution across all best practice Galaxy tools without requiring extra work by tool authors or administrators.

avatar for John Chilton

John Chilton

Galaxy Project, Penn State University

Thursday June 29, 2017 10:00 - 10:20
Einstein Auditorium Le Corum, Level 0

Attendees (27)