Purdue University

Commands

• R
• Rscript
• gridss
• gridss_annotate_vcf_kraken2
• gridss_annotate_vcf_repeatmasker
• gridss_extract_overlapping_fragments
• gridss_somatic_filter
• gridsstools
• virusbreakend
• virusbreakend-build

Module

You can load the modules by:

module load biocontainers
module load gridss

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 Gridss on our clusters:

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

module --force purge
ml biocontainers gridss