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Re: [gwl-devel] Next steps for the GWL
From: |
zimoun |
Subject: |
Re: [gwl-devel] Next steps for the GWL |
Date: |
Mon, 3 Jun 2019 17:16:13 +0200 |
Hi Ricardo,
On Wed, 29 May 2019 at 16:41, Ricardo Wurmus
<address@hidden> wrote:
>
> I’m going to use the GWL in the next few days to rewrite the PiGx RNAseq
> pipeline from Snakemake. This will likely show me what features are
> still missing from the GWL and what implemented features are awkward to
> use.
Awesome!
> * tighter integration with Guix features, e.g. to export a container
> image per process via “guix pack” or to pack up the whole workflow as
> a relocatable executable.
Yes! Awesome.
Relocatable tarballs. Docker images. Singularity one.
And maybe generate one pack (docker) per process and something to glue
together, e.g.,
http://www.genouest.org/godocker/
> * explore the use of inferiors — the GWL should be usable with any
> version of Guix that may be installed, not just the version that was
> used at compilation time. Can we use “guix repl” and inferiors,
> perhaps?
For reproducibility, a Guix commit should be provided and a `guix
pull` (inferiors) should be used.
For example, the output of `guix describe -f channels` should be used,
either with an option, either directly in the Scheme/Wisp workflow
file with a new keyword.
>
> * add support for executing processes in isolated environments
> (containers) — this requires a better understanding of process inputs.
Maybe this is the same story than the GoDocker above.
Talking about ideas:
- what about the Content Adressable Store?
- what about a bridge with CWL?
Thank you to revive the list. :-)
All the best,
simon
- Re: [gwl-devel] Next steps for the GWL,
zimoun <=