How to submit consecutive bash jobs using another job with a loop

Question

I have to phase (using shapeit software) 29 chromosomes, so it would be great if a could send a job that call another, the names of the files are the same, only change the chromosome number. Example phase.sh

#!/bin/bash
shapeit \
-P chr_1.ped chr_1.map \
--duohmm \
--rho 0.01 \
-O chr_1.phased 

I would need something like another job calling it

#!/bin/bash
for chr 1...29 
sbatch --phase.sh 
done

Thank you very much

Answer 1

Assuming you can change the first script to something like

#!/bin/bash
shapeit \
  -P "$1".ped "$1".map \
  --duohmm \
  --rho 0.01 \
  -O "$1".phased

and call it sbatch (or is that phase.sh?), you can then call it with

for chr in {1..29}; do
  sbatch --phase.sh "chr_$chr"
done

Of course, a better design might be to change the first script to run a loop over the arguments you pass it;

for chr; do
  shapeit \
    -P "$chr".ped "$chr".map \
    --duohmm \
    --rho 0.01 \
    -O "$chr".phased
done

and then call it like

thatscript chr_{1..29}