ResFinder identifies acquired genes and/or finds chromosomal / mutations mediating antimicrobial resistance in total or / partial DNA sequence of bacteria.
See versions that are available:
$ module avail resfinder
Load one version into your environment and run it:
$ module load resfinder/4.7.2 $ python -m resfinder
Notes from the sysadmin during installation.
$ sudo mkdir -p /export/apps/resfinder/4.7.2 $ sudo chown aorth /export/apps/resfinder/4.7.2 $ module load python/3.10 $ python -m venv /export/apps/resfinder/4.7.2/.venv $ source /export/apps/resfinder/4.7.2/.venv/bin/activate $ python -m pip install resfinder==4.7.2 $ cd /var/scratch $ git clone https://bitbucket.org/genomicepidemiology/resfinder_db $ git clone https://bitbucket.org/genomicepidemiology/pointfinder_db $ git clone https://bitbucket.org/genomicepidemiology/disinfinder_db $ sudo cp -r *_db /export/apps/resfinder/4.7.2 $ sudo chown -R root:root /export/apps/resfinder/4.7.2