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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. ;-)
[*] 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