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

[zimoun <zimon.toutoune@gmail.com>]

Hi (again) Josh :-)

On Mon, 2 Dec 2019 at 19:38, Josh Marshall
<joshua.r.marshall.1991@gmail.com> 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. ;-)

[*] https://guixwl.org/


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

[#] https://hpc.guix.info/blog/2019/01/creating-a-reproducible-workflow-with-cwl/

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.
simon

[1] https://www.nextflow.io/
[2] https://snakemake.readthedocs.io/en/stable/
[3] https://www.commonwl.org/
[4] http://www.openwdl.org/
[5] https://srfi.schemers.org/srfi-119/srfi-119.html