[rb-general] Paper preprint: Reproducible genomics analysis pipelines with GNU Guix

Roel Janssen roel at gnu.org
Wed Apr 11 23:16:19 CEST 2018

Ricardo Wurmus <rekado at elephly.net> writes:

> Hey all,
> I’m happy to announce that the group I’m working with has released a
> preprint of a paper on reproducibility with the title:
>     Reproducible genomics analysis pipelines with GNU Guix
>     https://www.biorxiv.org/content/early/2018/04/11/298653
> We built a collection of bioinformatics pipelines and packaged them with
> GNU Guix, and then looked at the degree to which the software achieves
> bit-reproducibility (spoiler: ~98%), analysed sources of non-determinism
> (e.g. time stamps), discussed experimental reproducibility at runtime
> (e.g. random number generators, kernel+glibc interface, etc) and
> commented on the idea of using “containers” (or application bundles)
> instead.
> The middle section is a bit heavy on genomics to showcase the features
> of the pipelines, but I think the introduction and the
> discussion/conclusion may be of general interest.

This looks really great!  I also like how you leverage GNU Autotools.

Finally there is a paper that uses GNU Guix as deployment tool for
scientific purposes. :)

Kind regards,
Roel Janssen

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