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phac-nml / staramr

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.
Apache License 2.0
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bioconda dependencies #133

Closed pmenzel closed 2 years ago

pmenzel commented 2 years ago

After fighting for a while with installing staramr via bioconda, I figured out that the latest versions of blast and pandas cause issues with staramr.

It worked after manually setting the environment like this:

dependencies:
  - pandas=1.1.5
  - bioconda::staramr=0.7.2
  - bioconda::blast=2.9.0

So maybe this needs to be reflected in https://github.com/bioconda/bioconda-recipes/blob/master/recipes/staramr/meta.yaml or staramr needs an update to work with latest versions of these tools.

apetkau commented 2 years ago

Thank you for bringing this up. I will have to look into what's going on with these dependencies.

apetkau commented 2 years ago

This was fixed in the bioconda recipe for release 0.7.2 a little while ago. The restriction on the version of pandas has also been fixed in PR #146