pathoscope

Species identification and strain attribution with unassembled sequencing data.

• Version: 2.0.7
• Added: March, 2022
• Link: https://github.com/PathoScope/PathoScope

See which versions are available:

$ module avail pathoscope

Load one version into your environment and run it:

$ module load pathoscope/2.0.7
$ pathoscope -h

Notes from the sysadmin during installation:

$ cd /tmp
$ wget https://github.com/PathoScope/PathoScope/archive/refs/tags/v2.0.7.tar.gz
$ tar xf v2.0.7.tar.gz
$ cd PathoScope-2.0.7
$ module load python/2.7
$ sudo mkdir -p /export/apps/pathoscope/2.0.7
$ sudo chown aorth /export/apps/pathoscope/2.0.7
$ python -m virtualenv /export/apps/pathoscope/2.0.7
$ source /export/apps/pathoscope/2.0.7/bin/activate
$ pip install .
$ sudo chown -R root:root /export/apps/pathoscope/2.0.7