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We show how Nix, a next generation cross-platform package manager, cleanly solves a number of reproducibility headaches in bioinformatics and computational biology.
Nix can easily create and manage isolated environments – like tools such as (mini)conda – and with our transparent and lightweight extensions can also succinctly describe computational pipelines, manage their execution in HPC environments or in parallel across a collection of machines, and produce portable containers (Docker or Singularity images).
Nix has an extensive package collection, which includes the whole of CRAN and Bioconductor, and while it lacks Bioconda's coverage of standalone bioinformatics tools, we show that Bioconda can be used within Nix expressions with some loss of the reproducibility guarantees.
We will succinctly specify a typical bioinformatics pipeline, and demonstrate how it can be executed in whole or in part on an HPC queuing system.
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