all messages for Guix-related lists mirrored at yhetil.org
 help / color / mirror / code / Atom feed
From: Matthieu Simonin <matthieu.simonin@inria.fr>
To: 57136@debbugs.gnu.org
Subject: bug#57136: Snakemake cannot execute remote jobs
Date: Thu, 25 Aug 2022 13:14:13 +0200	[thread overview]
Message-ID: <c5333f95-b977-c16b-953b-5033b8eac905@inria.fr> (raw)
In-Reply-To: <m1sfm32mxv.fsf@fastmail.net>

Hi there,

I've taken a stab at using it and restoring the patch as Konrad pointed seems the way to go.

But I also found that the package definition doesn't follow the guidelines[1] regarding the inputs definition.
One should use `propagated-inputs` instead of `inputs` for a python package.

In the current situation we can't invoke `snakemake` as a module:
`python -m snakemake` fails as the input dependencies aren't linked in the guix profile.

This way of invoking snakemake is used internally by snakemake here and there (for instance when calling the unit tests 
generated by `snakemake --generate-unit-tests`[2][3].

[1]: https://guix.gnu.org/manual/en/html_node/package-Reference.html
[2]: https://snakemake.readthedocs.io/en/stable/snakefiles/testing.html
[3]: https://github.com/snakemake/snakemake/blob/v7.7.0/snakemake/unit_tests/templates/ruletest.py.jinja2




  reply	other threads:[~2022-08-26 14:00 UTC|newest]

Thread overview: 5+ messages / expand[flat|nested]  mbox.gz  Atom feed  top
2022-08-11  8:39 bug#57136: Snakemake cannot execute remote jobs Konrad Hinsen
2022-08-25 11:14 ` Matthieu Simonin [this message]
2022-08-25 18:26 ` Konrad Hinsen
2022-08-25 18:50   ` Konrad Hinsen
2022-08-29 16:50 ` Konrad Hinsen

Reply instructions:

You may reply publicly to this message via plain-text email
using any one of the following methods:

* Save the following mbox file, import it into your mail client,
  and reply-to-all from there: mbox

  Avoid top-posting and favor interleaved quoting:
  https://en.wikipedia.org/wiki/Posting_style#Interleaved_style

* Reply using the --to, --cc, and --in-reply-to
  switches of git-send-email(1):

  git send-email \
    --in-reply-to=c5333f95-b977-c16b-953b-5033b8eac905@inria.fr \
    --to=matthieu.simonin@inria.fr \
    --cc=57136@debbugs.gnu.org \
    /path/to/YOUR_REPLY

  https://kernel.org/pub/software/scm/git/docs/git-send-email.html

* If your mail client supports setting the In-Reply-To header
  via mailto: links, try the mailto: link
Be sure your reply has a Subject: header at the top and a blank line before the message body. 
Code repositories for project(s) associated with this external index

	https://git.savannah.gnu.org/cgit/guix.git

This is an external index of several public inboxes,
see mirroring instructions on how to clone and mirror
all data and code used by this external index.