Rosen Center for Advanced Computing
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Software: CFSAN SNP Pipeline

Description

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.

Available Versions

Unspecified: 2.2.1

Docker hub: https://hub.docker.com/r/staphb/cfsan-snp-pipeline
Home page: https://github.com/CFSAN-Biostatistics/snp-pipeline

Commands

  • cfsan_snp_pipeline

Module

You can load the modules by:

module load biocontainers
module load cfsan-snp-pipeline

Example job

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run cfsan-snp-pipeline on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=cfsan-snp-pipeline
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers cfsan-snp-pipeline