Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.
See which versions are available:
$ module avail rgi
Load one version into your environment and run it:
$ module load rgi/6.0.2 $ rgi
Notes from the sysadmin during installation:
$ cd /tmp $ https://github.com/arpcard/rgi/archive/refs/tags/6.0.2.tar.gz $ tar xf 6.0.2.tar.gz $ cd rgi-6.0.2 $ sudo mkdir -p /export/apps/rgi/6.0.2 $ sudo chown aorth:aorth /export/apps/rgi/6.0.2 $ python3 -m venv /export/apps/rgi/6.0.2/.venv $ source /export/apps/rgi/6.0.2/.venv/bin/activate $ pip install --upgrade pip setuptools wheel $ pip install -r requirements.txt $ python setup.py build $ python setup.py test $ python setup.py install
Still not sure if there are any datasets/databases we need to set up, or if the included tests are supposed to pass…