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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.



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
snp-pipeline-software.txt · Last modified: 2019/01/29 13:53 by aorth