SNP Pipeline

The CFSAN SNP Pipeline is a Python-based system for the production of SNP matrices from sequence data used in the phylogenetic analysis of pathogenic organisms sequenced from samples of interest to food safety.

• Version: 1.0.1
• Added: June, 2018
• Updated: January, 2019
• Link: https://snp-pipeline.readthedocs.io/en/latest/installation.html

See which versions of snp-pipeline are available:

$ module avail snp-pipeline

Load snp-pipeline into your environment:

$ module load snp-pipeline/1.0.1

Notes from the sysadmin during installation:

$ module load python/3.5
$ sudo mkdir -p /export/apps/snp-pipeline/1.0.1
$ sudo chown aorth /export/apps/snp-pipeline/1.0.1
$ python -m venv /export/apps/snp-pipeline/1.0.1
$ . /export/apps/snp-pipeline/1.0.1/bin/activate
$ pip install --upgrade pip setuptools
$ pip install snp-pipeline==1.0.1
$ sudo chown -R root:root /export/apps/snp-pipeline/1.0.1