====== 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.

===== Information =====

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

===== Usage =====

See which versions of snp-pipeline are available:
<code>$ module avail snp-pipeline</code>

Load snp-pipeline into your environment:
<code>$ module load snp-pipeline/1.0.1</code>

===== Installation ======

Notes from the sysadmin during installation:

<code>$ 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</code>