Bioinformatics Seminar

Time:
Venue: Na

4 December 2018

Bionix: Highly reproducible functional bioinformatics
Unifying packages

Justin Bedo
WEHI Bioinformatics

containers ; and workflow managers;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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The Walter and Eliza Hall Institute of Medical Research