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iqbal-lab-org / pling

Plasmid analysis using rearrangement distances
MIT License
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Switch rule gen_minimap_input to use conda environment instead of a container #49

Closed leoisl closed 3 months ago

leoisl commented 7 months ago

See https://github.com/iqbal-lab-org/pling/blob/7dbd4877183fc07e133f4d2ea0ffcfa1dd237d7c/pling/anno_snakemake/Snakefile#L77-L78

I switched to container because I was having issues installing bakta through conda, but I should have dug deeper and kept the conda env. Note that we also need to change the gen_minimap_input.py script to have a CLI and be callable from shell. Doing this will remove having singularity as a dependency, which is worth it

babayagaofficial commented 3 months ago

Fixed in v1.0.3