Stable 1.0.0#152
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* Strip .fq suffix in regex operation * Set --retries type to int. Previously it was interpreted as a str, which caused errors.
Fix Docs
* Removed redundant line including src/mmaseq/utils which occationally caused a pip install dupplication err * Removed redundant force includion of the data/reads.url which is allready included
Hatchling, by default, already includes sub-packages, so mmaseq/utils was listed twice. This caused issues during re-installation. The fix is to remove the unnecessarily duplicated entry.
In BioConda, bcftools and kleborate both incorrectly lists in their deps gls >2.7. However, they both are compiled against either gsl 2.6 or 2.5, both of which (confusingly) uses the shared object libgsl.so.25. I'm not completely sure why this workaround works, but it's possible that this causes both v2.7 and v2.5 to be installed, which works file as only v2.5 is needed at runtime. The real fix is an upstream fix to BioConda's deps, but this issue is more than four years old, so don't hold your breath.
The command used to `-v`, but newer versions require `--version`. This fix is a bandaid fix - a better solution is to pin versions of deps.
Before, versions.py would try to import Conda in order to list every env in the deploy dir. However, this required the Python process to run in an env with the Conda Python API available, and this was not listed in pyproject.toml as a dependency. And, since Conda cannot be installed via pip, it could not easily be added as a dependency. Instead, use the Conda CLI to do the same thing. This works, because, since MMASeq must run in a Conda env, the env var CONDA_EXE should exist, and point to an existing Conda binary.
Various fixes
Minor fixes
Fixed pip installation duplication err Removed redundant force-include
Added vancomycin
* Pointfinder does not always produce output file so it has been separated to separate rule to avoid erronous smk errors on missing output files * Same goes for Disinfinder * Tool running msg's fixed to rule name
…d a conda executable Fix#136 and Fix#139
Fix: Separated Point and Disinfinder and log polish
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