csvtk
Link to section 'Introduction' of '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.
Link to section 'Versions' of 'csvtk' Versions
- 0.23.0
- 0.25.0
Link to section 'Commands' of 'csvtk' Commands
- csvtk
Link to section 'Module' of 'csvtk' Module
You can load the modules by:
module load biocontainers
module load csvtk
Link to section 'Example job' of '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