Purdue University

Commands

• csvclean
• csvcut
• csvformat
• csvgrep
• csvjoin
• csvjson
• csvlook
• csvpy
• csvsort
• csvsql
• csvstack
• csvstat
• in2csv
• sql2csv

Module

You can load the modules by:

module load biocontainers
module load csvkit

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 csvkit on our clusters:

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

module --force purge
ml biocontainers csvkit