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.
--
Ricardo
GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC
https://elephly.net
