Bioinformatics Seminars

Bioinformatics Seminar

Time: 10:45am Tuesdays.
Venue:
Level 7 Seminar Room 2, WEHI1

4 December 2018

Bionix: Highly reproducible functional bioinformatics
Unifying packages, containers, and workflow managers

Justin Bedo
WEHI Bioinformatics

A challenge for bioinformaticians is to make our computations reproducible -
that is, easy to (re)run, combine, and share, while also guaranteed to generate
the same results. We present bionix, a highly reproducible yet very simple
functionl pipeline specification language built on top of the Nix package
manager. We show how one unified framework overcomes reproducibility problems
usually tackled with a combination of package managers (e.g., Conda), containers
(e.g., Docker, Singularity), workflow engines (e.g., Toil, Ruffus) and languages
(e.g., WDL, CWL). Because of the design of Nix, we have stronger reproducibility
guarantees then that obtained with commonly used technologies. Bionix pipelines
can seamlessly execute builds directly, on remote machines (e.g., cloud
computing), or via HPC queuing systems.



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