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

[Amirouche Boubekki]

Wow very great, thanks for sharing.

On Wed, Apr 11, 2018 at 11:17 PM Roel Janssen <roel at gnu.org> wrote:

>
> 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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