I would like to run a command for each entry in a column of a file. I am currently doing the following, but am getting an ambiguous redirect error.
while read -r entry; do cmd "$entry" ; done < $(cut -f2 file.tsv)
I've also tried
done <(cut -f2 file.tsv)
which throws an unexpected token syntax error.
What is the correct syntax for doing this?
A tab separated values file with file paths in the column of interest.
1 file1.txt ... 2 file2.txt ... 3 file3.txt ...
The script should run the commands
cmd file1.txt cmd file2.txt cmd file3.txt
For the purpose of a simple example, you can use
cat as the
cmd, since the error is not with the
cmd per se, but with the input redirection.
The actual command I am running is the bioinformatics tool kallisto, specifically