fix: Only --bind Snakemake module into container when we're working with a Python script #1206
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johanneskoester
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Oct 11, 2021
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Can you please format your PR with black? |
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Done |
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Nov 15, 2021
…nakemake#1206) Co-authored-by: Johannes Köster <johannes.koester@uni-due.de>
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Why is bind needed for Python scripts? Is it only necessary for importing logger from snakemake.logging? |
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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
snakemakenamespace 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.