Chain a bunch of Torque/PBS jobs together, pulling arguments from a config file

job_chainer.sh

#!/bin/bash

#chain some torque jobs together with dependencies

#set parameters
start_job=$1
start_index=0
end_index=41
conf_file=/home/wtb2/Documents/em_analysis.conf
#read config file
IFS=$'\n' read -d  '' -r -a conf < $conf_file
for i in `seq $start_index $end_index`
do
        #write to temporary file
        echo "/home/wtb2/Documents/EBTEL_analysis/bin/ebtel_dem_analysis_main.py "${conf[$(($i))]} > tmp_queup
        chmod u+x tmp_queup
        if [[ $i -eq $start_index ]]; then
                qsub -N "em_analysis_${i}" -j oe ./tmp_queup
        else
                qsub -N "em_analysis_${i}" -j oe -W depend=afterok:$(($start_job+$i-$start_index-1)) ./tmp_queup
        fi
done