ILRI Research Computing

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====== resfinder ======
ResFinder identifies acquired genes and/or finds chromosomal / mutations mediating antimicrobial resistance in total or / partial DNA sequence of bacteria.

===== Information =====

  * Version: 4.6.0
  * Added: March, 2025
  * Link: https://pypi.org/project/resfinder

===== Usage =====

See versions that are available:
<code>$ module avail resfinder</code>

Load one version into your environment and run it:
<code>$ module load resfinder/4.6.0
$ python -m resfinder</code>


===== Installation ======
Notes from the sysadmin during installation.

<code>$ sudo mkdir -p /export/apps/resfinder/4.6.0
$ sudo chown aorth:aorth /export/apps/resfinder/4.6.0
$ python3 -m venv /export/apps/resfinder/4.6.0
$ source /export/apps/resfinder/4.6.0/bin/activate
$ python3 -m pip install -U pip setuptools wheel
$ python3 -m pip install resfinder==4.6.0
$ 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
$ cp -r *_db /export/apps/resfinder/4.6.0
$ sudo chown -R root:root /export/apps/resfinder/4.6.0</code>