Software: Csvtk
Description
Csvtk is a cross-platform, efficient and practical CSV/TSV toolkit.
Available Versions
Unspecified: | 0.23.0 0.25.0 |
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For more information, please check its website: https://biocontainers.pro/tools/csvtk and its home page on Github.
Commands
- csvtk
Module
You can load the modules by:
module load biocontainers
module load csvtk
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 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