bug#57136: Snakemake cannot execute remote jobs

bug#57136: Snakemake cannot execute remote jobs

[Konrad Hinsen]

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which is outdated.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

bug#57136: Snakemake cannot execute remote jobs

[Matthieu Simonin]

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

bug#57136: Snakemake cannot execute remote jobs

[Konrad Hinsen]

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

bug#57136: Snakemake cannot execute remote jobs

[Konrad Hinsen]

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

bug#57136: Snakemake cannot execute remote jobs

[Konrad Hinsen]

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