GNU bug report logs - #57136
Snakemake cannot execute remote jobs

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Package: guix;

Reported by: Konrad Hinsen <konrad.hinsen <at> fastmail.net>

Date: Thu, 11 Aug 2022 08:41:02 UTC

Severity: normal

Done: Konrad Hinsen <konrad.hinsen <at> fastmail.net>

Bug is archived. No further changes may be made.

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From: help-debbugs <at> gnu.org (GNU bug Tracking System)
To: Konrad Hinsen <konrad.hinsen <at> fastmail.net>
Subject: bug#57136: closed (Re: Snakemake cannot execute remote jobs)
Date: Mon, 29 Aug 2022 16:51:02 +0000

[Message part 1 (text/plain, inline)]
Your bug report

#57136: Snakemake cannot execute remote jobs

which was filed against the guix package, has been closed.

The explanation is attached below, along with your original report.
If you require more details, please reply to 57136 <at> debbugs.gnu.org.

-- 
57136: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=57136
GNU Bug Tracking System
Contact help-debbugs <at> gnu.org with problems

[Message part 2 (message/rfc822, inline)]
From: Konrad Hinsen <konrad.hinsen <at> fastmail.net>
To: 57136-done <at> debbugs.gnu.org
Subject: Re: Snakemake cannot execute remote jobs
Date: Mon, 29 Aug 2022 18:50:41 +0200

The bug is fixed via the patch referenced above in commit 5831155175614726685edab7efa60ce48e4da1f5.


[Message part 3 (message/rfc822, inline)]
From: Konrad Hinsen <konrad.hinsen <at> fastmail.net>
To: bug-guix <at> gnu.org
Subject: Snakemake cannot execute remote jobs
Date: Thu, 11 Aug 2022 10:39:56 +0200

The execution of Snakemake workflows fails on a cluster because the
script that Snakemake executes remotely does not reference Python
correctly.

This is due to a patch applied in the Guix package
definition (build phase call-wrapper-not-wrapped-snakemake, 
https://git.savannah.gnu.org/cgit/guix.git/tree/gnu/packages/python-xyz.scm#n9713)
which is outdated. The corresponding code in Snakemake was changed
significantly in the following commit:

  https://github.com/snakemake/snakemake/commit/e87cc979bea0567e1cd97722d385f472857df83c#diff-438f3317205fd7130727d0589d2fc1a6c2e1f6fc48c2c04d354a8a09b91ba2f4

Cheers,
  Konrad
This bug report was last modified 2 years and 262 days ago.

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