This happens because PlasmidFinder v2 uses the distutils stdlib, which was removed in Python v3.12.
Since MMASeq requires Python 3.13 and installs PlasmidFinder v2, MMAseq does not work currently.
I recommend moving from PlasmidFinder v2 to v3. To do this requires:
- Changing the plasmidfinder env YAML file to install v3 via pip, since v3 is not on bioconda
- PlasmidFinder v3 currently does not add an executable to the PATH. So, invoke it with
python -m plasmidfinder.
- PlasmidFinder v3 is a breaking change. In particular, the output changed. So, mmaseq would have to parse its output differently.
An alternative is to maintain a patch of PlasmidFinder v2, but I would think that's too annoying.
This happens because PlasmidFinder v2 uses the distutils stdlib, which was removed in Python v3.12.
Since MMASeq requires Python 3.13 and installs PlasmidFinder v2, MMAseq does not work currently.
I recommend moving from PlasmidFinder v2 to v3. To do this requires:
python -m plasmidfinder.An alternative is to maintain a patch of PlasmidFinder v2, but I would think that's too annoying.