Linux/Unix clusters with qsub utility

If you have a cluster with qsub utility to submit jobs, you have to write two short scripts. The first one will just loop on chromosome and submit the job to the cluster for the current chromosome,

$cat NMQsubHmm.sh
#!/bin/bash

QUE = $1
# man qsub to obtain an explanation of the options
for i in "I" "II" "III" "IV" "V" "VI" "VII" "VIII" \
         "IX" "X" "XI" "XII" "XIII" "XIV" "XV" "XVI"
do
   qsub -m b -m e -e ./chr${i}.err -q $QUE -o ./chr${Roman}.out ./NMQsubHmmRun.sh chr${i}
done

where the program takes as single argument the name of the queue where you want to submit all your jobs (note that chr${i} is the name of the chromosome, so modify the elements of the loop or the stem name (chr) if the sequence names are different). The second program is a very short piece of code that just call NMhmmfit (to modify if you want to use different arguments that the one specified by default).

$cat NMQsubHmmRun.sh
#!/bin/bash
#$ -cwd
#$ -V

chr=$1
#
NMhmmfit -i ./data.db -o NMhmmfit -c ${chr}