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snp-pipeline-software

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

Usage

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

Installation

Notes from the sysadmin during installation:

$ cd /tmp
$ module load python/3.5.3
$ sudo mkdir -p /export/apps/snp-pipeline/1.0.1
$ sudo chown -R aorth: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
$ pip3 install --upgrade pip setuptools
$ pip3 install snp-pipeline
$ sudo chown -R root:root /export/apps/snp-pipeline/1.0.1
snp-pipeline-software.txt · Last modified: 2018/06/01 20:58 by aorth