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

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

SUBMITTER: Bedo J 

PROVIDER: S-EPMC7672450 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature