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Re: [rb-general] Paper preprint: Reproducible genomics analysis pipeline

From: Ludovic Courtès
Subject: Re: [rb-general] Paper preprint: Reproducible genomics analysis pipelines with GNU Guix
Date: Fri, 11 May 2018 10:10:19 +0200
User-agent: Gnus/5.13 (Gnus v5.13) Emacs/25.3 (gnu/linux)


Ricardo Wurmus <address@hidden> skribis:

> Ludovic Courtès <address@hidden> writes:


>> 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 ‘’ 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.
> I think a higher level “” file would be of great help.  In
> general, independent of this particular use case.

Perhaps we could add to Autoconf-Archive (if it doesn’t have such things
already) macros to deal with the R and Python stuff you had to deal
with?  And then publish a simple template that people could use as a
starting point.

> There is a danger in pushing all of this work to Guix, though.  One of
> the great features of the Autotools suite is that users don’t need to
> know about it.  If we assume that users have Guix (which in our paper we
> only strongly encourage) we might as well have implemented the whole
> pipeline using the Guix Workflow Language.  This is, of course, a valid
> option, but the goal of the paper was to demonstrate a more general
> claim and approach to designing pipelines.  I wanted to encourage
> pipeline developers to treat their pipeline as a first-class package,
> not as some glue code that binds together tools in a specially crafted
> runtime environment.

Yes, that makes sense.

> I think that this alternative is worth exploring, though.  Building a
> complex pipeline with the Guix Workflow Language that addresses both
> deployment and execution order would be an interesting project; it would
> also be good to look into ways to make such a workflow available to
> users who do not have the ability or intention to install Guix.  An easy
> way is to bundle up the whole environment as one giant container blob,
> but I think we can do better.  I’d love to collaborate with other users
> of the GWL to see how far we can push it.

Would be nice, indeed.


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