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phac-nml / irida-plugin-amr-detection

IRIDA Plugin for AMR Detection
Apache License 2.0
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RGI not producing AMR results #9

Closed apetkau closed 3 years ago

apetkau commented 4 years ago

For some reason, with new installs of RGI (version 4.2.2), no AMR results are ever found. This occurs even for the example I have in the github documentation SRR8914694 which should have results.

apetkau commented 4 years ago

I suspect there are differences in dependencies being installed by conda, leading to this issue.

apetkau commented 4 years ago

This is caused by conda installing too recent of a version of biopython (intalling version 1.74, instead of 1.72). This is listed in the issue here https://github.com/arpcard/rgi/issues/58.

Solution (for now) is to activate the Galaxy RGI environment and manually downgrade biopython:

conda activate __rgi@4.2.2
conda install biopython=1.72

A permanent fix would be to update the bioconda recipe to pin to that version of biopython.

apetkau commented 3 years ago

Fixed in release 0.2.0 - https://github.com/phac-nml/irida-plugin-amr-detection/releases/tag/0.2.0