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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.


> * 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.,

> * 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,

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