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

[Ludovic Courtès]

Hello Ricardo & all!

Ricardo Wurmus <address@hidden> skribis:

> 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.

Very impressive piece of work!  I think it’s important to stress that
reproducible builds is a crucial foundation for reproducible
computational experiments, and this paper does a great job at this.

Also nice that you show you can have these bit-reproducible pipelines
formalized in Guix *and* produce a ready-to-use “container image.”

Hopefully we can soon address the remaining sources of non-determinism
shown in Table 3 (I think you already addressed some of them in the
meantime, didn’t you?).

The bit I’m less comfortable with is Autotools.  I do understand how it
helps capture configure-time dependencies, and how it generally helps
people package and use the software; I think it’s one of the best tools
for the job.  However it’s also hard to learn and, whether it’s
justified or not, it’s considered “scary.”

Given the intended audience, I wonder how we could provide a simpler
path to achieve the same goal.  It could be a set of Autoconf macros
leading to high-level ‘configure.ac’ files without any line of shell
code, or it could be Guix interpreting a top-level .scm or JSON file,
both of which would ideally be easier to write for bioinformaticians.

What are your thoughts on this?

Anyway, kudos on this, thank you!

Ludo’.