Unifying package managers, workflow engines, and containers: Computational reproducibility with BioNix
- Author(s)
- Bedő, J; Di Stefano, L; Papenfuss, AT;
- Details
- Publication Year 2020-11-18,Volume 9,Issue #11,Page giaa121
- Journal Title
- Gigascience
- Publication Type
- Journal Article
- 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 expression language and is released on GitHub under the 3-clause BSD license: https://github.com/PapenfussLab/bionix (biotools:BioNix) (BioNix, RRID:SCR_017662).
- Publisher
- Oxford Academic
- Research Division(s)
- Bioinformatics
- PubMed ID
- 33205815
- Publisher's Version
- https://doi.org/10.1093/gigascience/giaa121
- Open Access at Publisher's Site
https://doi.org/10.1093/gigascience/giaa121- Terms of Use/Rights Notice
- Refer to copyright notice on published article.
- Documents
Creation Date: 2021-02-01 12:07:24
Last Modified: 2021-03-02 02:09:37