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fix: Only --bind Snakemake module into container when we're working with a Python script #1206

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merged 2 commits into from Oct 21, 2021

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frankier
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@frankier frankier commented Oct 7, 2021

Description

By default Snakemake binds its Python module into the container, but this is only needed for Python script mode.

This is problem if Snakemake is already running inside a Singularity container, as I am experimenting with at https://github.com/frankier/singslurm2 then the Snakemake module is not available on the host when executing.

This patch makes it so the bind is only made when we actually need to run a Python script.

Long term, I would favor a situation where the snakemake namespace available to Python scripts was more like a data file, which can somehow be shimmed directly into the script, like the current RustScript implementation --- assuming this is possible. This would seem to allow more flexibility for combining the Singularity implementation with other stuff.

@frankier frankier requested a review from johanneskoester as a code owner Oct 7, 2021
@frankier frankier force-pushed the only-bind-for-python-script branch from 2286cd7 to 99b2608 Compare Oct 7, 2021
@frankier frankier changed the title Only --bind Snakemake module into container when we're working with a Python script fix: Only --bind Snakemake module into container when we're working with a Python script Oct 7, 2021
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@johanneskoester johanneskoester left a comment

Thanks. And yes, I agree about the snakemake object.

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johanneskoester commented Oct 11, 2021

Can you please format your PR with black?

@frankier frankier force-pushed the only-bind-for-python-script branch from 99b2608 to 35a8960 Compare Oct 11, 2021
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frankier commented Oct 11, 2021

Done

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sonarcloud bot commented Oct 21, 2021

Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

No Coverage information No Coverage information
0.0% 0.0% Duplication

@johanneskoester johanneskoester merged commit 1d79f62 into snakemake:main Oct 21, 2021
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pvandyken pushed a commit to pvandyken/snakemake that referenced this pull request Nov 15, 2021
…nakemake#1206)

Co-authored-by: Johannes Köster <johannes.koester@uni-due.de>
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2 participants