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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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Updated default commits to latest with ResFinder and PlasmidFinder #104

Closed jennifertran closed 3 years ago

jennifertran commented 4 years ago

Updated the default database versions to the latest commits. For ResFinder it's up until 2019-10-01 and the PlasmidFinder is updated to 2019-10-18. Had to change one of the test cases to accurately reflect the new changes.

Another thing that was updated was the ARG_drug_key files since this is how staramr identifies the name of the drug. I automated this update process by creating a script that converts either the resfinder or the plasmidfinder into tsv files given an excel sheet.

In order to run this program, set the command python update_staramr_db.py <file> <resfinder,pointfinder>. The script requires pandas, sys and xlrd>=1.0.0 as dependencies, I suggest creating a new conda environment for this script

apetkau commented 3 years ago

It looks like this PR is old enough that it's still assuming TravisCI will be run (it won't be, only Github actions). I am closing this PR and will re-open as a new PR which should hopefully fix the issue.