Csvkit¶
Introduction¶
csvkit is a suite of command-line tools for converting to and working with CSV, the king of tabular file formats.
For more information, please check:
Docker hub: https://hub.docker.com/r/johnyaku/csvkit
Home page: https://csvkit.readthedocs.io/en/latest/
Versions¶
1.1.1
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¶
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 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