Journal article

Unifying package managers, workflow engines, and containers: Computational reproducibility with BioNix.

Justin Bedo, Leon Di Stefano, Anthony T Papenfuss

GigaScience | BioMed Central | Published : 2020

Abstract

MOTIVATION: A challenge for computational biologists is to make our analyses reproducible-i.e. to rerun, combine, and share, with the assurance that equivalent runs will generate identical results. Current best practice aims at this using a combination of package managers, workflow engines, and containers. RESULTS: We present BioNix, a lightweight library built on the Nix deployment system. BioNix manages software dependencies, computational environments, and workflow stages together using a single abstraction: pure functions. This lets users specify workflows in a clean, uniform way, with strong reproducibility guarantees. AVAILABILITY AND IMPLEMENTATION: BioNix is implemented in the Nix ex..

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Grants

Awarded by Australian National Health and Medical Research Council (NHMRC)


Awarded by NHMRC


Funding Acknowledgements

A.T.P. was supported by the Lorenzo and Pamela Galli Charitable Trust and by an Australian National Health and Medical Research Council (NHMRC) Program Grant (1054618) and NHMRC Senior Research Fellowship (1116955). The research benefitted by support from the Victorian State Government Operational Infrastructure Support and Australian Government NHMRC Independent Research Institute Infrastructure Support. J.B. was supported by the Stafford Fox Medical Research Foundation.