* bug#57136: Snakemake cannot execute remote jobs
@ 2022-08-11 8:39 Konrad Hinsen
2022-08-25 11:14 ` Matthieu Simonin
` (2 more replies)
0 siblings, 3 replies; 5+ messages in thread
From: Konrad Hinsen @ 2022-08-11 8:39 UTC (permalink / raw)
To: 57136
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which is outdated.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
^ permalink raw reply [flat|nested] 5+ messages in thread* bug#57136: Snakemake cannot execute remote jobs 2022-08-11 8:39 bug#57136: Snakemake cannot execute remote jobs Konrad Hinsen @ 2022-08-25 11:14 ` Matthieu Simonin 2022-08-25 18:26 ` Konrad Hinsen 2022-08-29 16:50 ` Konrad Hinsen 2 siblings, 0 replies; 5+ messages in thread From: Matthieu Simonin @ 2022-08-25 11:14 UTC (permalink / raw) To: 57136 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 ^ permalink raw reply [flat|nested] 5+ messages in thread
* bug#57136: Snakemake cannot execute remote jobs 2022-08-11 8:39 bug#57136: Snakemake cannot execute remote jobs Konrad Hinsen 2022-08-25 11:14 ` Matthieu Simonin @ 2022-08-25 18:26 ` Konrad Hinsen 2022-08-25 18:50 ` Konrad Hinsen 2022-08-29 16:50 ` Konrad Hinsen 2 siblings, 1 reply; 5+ messages in thread From: Konrad Hinsen @ 2022-08-25 18:26 UTC (permalink / raw) To: 57136 I have submitted a patch that fixes this problem: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=57413 This is the patch that Matthieu referred to, and which he tested in a cluster environment. Cheers, Konrad ^ permalink raw reply [flat|nested] 5+ messages in thread
* bug#57136: Snakemake cannot execute remote jobs 2022-08-25 18:26 ` Konrad Hinsen @ 2022-08-25 18:50 ` Konrad Hinsen 0 siblings, 0 replies; 5+ messages in thread From: Konrad Hinsen @ 2022-08-25 18:50 UTC (permalink / raw) To: 57136 The other problem that Matthieu pointed out (but which is unrelated to the initial bug report) is fixed by the following two patches for snakemake-6 and snakemake-7: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=57414 https://debbugs.gnu.org/cgi/bugreport.cgi?bug=57415 Cheers, Konrad ^ permalink raw reply [flat|nested] 5+ messages in thread
* bug#57136: Snakemake cannot execute remote jobs 2022-08-11 8:39 bug#57136: Snakemake cannot execute remote jobs Konrad Hinsen 2022-08-25 11:14 ` Matthieu Simonin 2022-08-25 18:26 ` Konrad Hinsen @ 2022-08-29 16:50 ` Konrad Hinsen 2 siblings, 0 replies; 5+ messages in thread From: Konrad Hinsen @ 2022-08-29 16:50 UTC (permalink / raw) To: 57136-done The bug is fixed via the patch referenced above in commit 5831155175614726685edab7efa60ce48e4da1f5. ^ permalink raw reply [flat|nested] 5+ messages in thread
end of thread, other threads:[~2022-08-29 16:52 UTC | newest] Thread overview: 5+ messages (download: mbox.gz / follow: Atom feed) -- links below jump to the message on this page -- 2022-08-11 8:39 bug#57136: Snakemake cannot execute remote jobs Konrad Hinsen 2022-08-25 11:14 ` Matthieu Simonin 2022-08-25 18:26 ` Konrad Hinsen 2022-08-25 18:50 ` Konrad Hinsen 2022-08-29 16:50 ` Konrad Hinsen
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