#!/bin/bash

#where should the outputs be stored?
OutputDir="/fs/scratch/PAS0654/shell_demo/outputs"
echo '[ Processed file output directory: ' $OutputDir ' ]'
export OutputDir

#where is your executable compiled?
RunDir="/users/PAS0654/osu0673/A23_analysis/araROOT"
export RunDir

#define the list of runs to execute on
readfile=run_list.txt

counter=0
while read line1
do
	qsub -v RUNDIR=$RunDir,OUTPUTDIR=$OutputDir,FILE=$line1 -N 'job_'$counter run.sh
	counter=$((counter+1))
done < $readfile