Csvtk

Introduction

Csvtk is a cross-platform, efficient and practical CSV/TSV toolkit.

For more information, please check its website: https://biocontainers.pro/tools/csvtk and its home page on Github.

Versions

  • 0.23.0

  • 0.25.0

Commands

  • csvtk

Module

You can load the modules by:

module load biocontainers
module load csvtk

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 Csvtk on our clusters:

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

module --force purge
ml biocontainers csvtk

cat data.csv \
 |  csvtk summary --ignore-non-digits --fields f4:sum,f5:sum --groups f1,f2 \
 |  csvtk pretty