From: ludovic.courtes@inria.fr (Ludovic Courtès)
To: Ricardo Wurmus <rekado@elephly.net>
Cc: guix-devel <guix-devel@gnu.org>, "guix-hpc@gnu.org" <guix-hpc@gnu.org>
Subject: Re: [rb-general] Paper preprint: Reproducible genomics analysis pipelines with GNU Guix
Date: Fri, 11 May 2018 10:10:19 +0200 [thread overview]
Message-ID: <878t8qr4t0.fsf@inria.fr> (raw)
In-Reply-To: <87fu30fsra.fsf@elephly.net> (Ricardo Wurmus's message of "Wed, 09 May 2018 23:01:29 +0200")
Hello!
Ricardo Wurmus <rekado@elephly.net> skribis:
> Ludovic Courtès <ludovic.courtes@inria.fr> 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 ‘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.
>
> I think a higher level “configure.ac” 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.
Thanks,
Ludo’.
next prev parent reply other threads:[~2018-05-11 8:10 UTC|newest]
Thread overview: 13+ messages / expand[flat|nested] mbox.gz Atom feed top
2018-04-11 12:18 Paper preprint: Reproducible genomics analysis pipelines with GNU Guix Ricardo Wurmus
2018-04-11 18:30 ` [rb-general] " Holger Levsen
2018-04-11 18:40 ` Ricardo Wurmus
2018-04-11 19:00 ` Holger Levsen
2018-04-11 18:31 ` Holger Levsen
2018-04-11 21:16 ` Roel Janssen
2018-04-15 7:50 ` Amirouche Boubekki
2018-04-23 8:20 ` [rb-general] " Ludovic Courtès
[not found] ` <87fu30fsra.fsf@elephly.net>
2018-05-11 8:10 ` Ludovic Courtès [this message]
2018-05-11 8:19 ` Ricardo Wurmus
2018-05-11 9:39 ` Catonano
2018-05-13 5:07 ` Ricardo Wurmus
2018-05-13 8:58 ` Catonano
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