Introduction ~~~~~~~~ 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.
For more information, please check:
Docker hub: https://hub.docker.com/r/staphb/cfsan-snp-pipeline
Home page: https://github.com/CFSAN-Biostatistics/snp-pipeline
Docker hub: https://hub.docker.com/r/staphb/cfsan-snp-pipeline
Home page: https://github.com/CFSAN-Biostatistics/snp-pipeline
- 2.2.1
Commands ~~~~~~~ - cfsan_snp_pipeline
You can load the modules by:
module load biocontainers
module load cfsan-snp-pipeline
Example job ~~~~~ .. warning:: 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