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bug#57136: Snakemake cannot execute remote jobs
From: |
Matthieu Simonin |
Subject: |
bug#57136: Snakemake cannot execute remote jobs |
Date: |
Thu, 25 Aug 2022 13:14:13 +0200 |
User-agent: |
Mozilla/5.0 (X11; Linux x86_64; rv:91.0) Gecko/20100101 Thunderbird/91.12.0 |
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