snp-pipeline-software
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Table of Contents
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
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.1527875889.txt.gz · Last modified: 2018/06/01 17:58 by aorth