Table of Contents

rgi

Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.

Information

Usage

See which versions are available:

$ module avail rgi

Load one version into your environment and run it:

$ module load rgi/6.0.2
$ rgi

Installation

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…