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Re: How do I support building a guix package over multiple machines in a

From: zimoun
Subject: Re: How do I support building a guix package over multiple machines in a cloud environment?
Date: Mon, 2 Dec 2019 20:00:07 +0100

Hi (again) Josh :-)

On Mon, 2 Dec 2019 at 19:38, Josh Marshall
<address@hidden> wrote:

> He uses it as a bioinformatics workflow to generate some analysis.  It

GWL should work for this use case. o/

> Is this kind of use case supported?  If so, how so?  Is nextflow not
> practical to keep?  Please, someone catch me up here so I can start to
> write code to help him out.  If this goes well, my company could
> integrate for gwl/guix in our work, which would be amazing.

Netxflow [1] is a Domain Specific Language (DSL): you write "rules"
and how these rules are combined together. In the bioinformatics
field, Snakemake [2] seems more popular. Other alternatives are CWL
[3], WDL [4], etc.

Basically, you describe:
 - what is the inputs
 - what is the outputs
 - how to process the inputs to produce the outputs

You can find examples there [*]. It uses the WISP syntax [5] but it
perfectly works with a Scheme-syntax if you prefer parenthesis. ;-)


However, you should be interested by this blog post [#] by Pjotr using
Guix and CWL and other niceties!


AFAIK, Nextflow is not yet packaged in Guix. One direction is to
package it and then use the workflow described in Nextflow DSL in the
spirit of [#]. One other direction is to rewrite the workflow using
the GWL DSL. It depends a bit on what is your final aim.

Hope that helps.


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