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>
Cc: tracker <at> debbugs.gnu.org
Subject: bug#57136: closed (Snakemake cannot execute remote jobs)
Date: Mon, 29 Aug 2022 16:51:02 +0000

[Message part 1 (text/plain, inline)]
Your message dated Mon, 29 Aug 2022 18:50:41 +0200
with message-id <m1fshfdme6.fsf <at> fastmail.net>
and subject line Re: Snakemake cannot execute remote jobs
has caused the debbugs.gnu.org bug report #57136,
regarding Snakemake cannot execute remote jobs
to be marked as done.

(If you believe you have received this mail in error, please contact
help-debbugs <at> gnu.org.)


-- 
57136: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=57136
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[Message part 2 (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which is outdated.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



[Message part 3 (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.
This bug report was last modified 2 years and 261 days ago.

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