submit-align-overlapping-projects-pair-jobs-if-not-exists

#!/bin/bash

# Submit jobs to align pairs of overlapping projects for all ranges where
# rigid.txt does not exist (where the job had failed earlier)
#
# Call:
#       ./submit-align-overlapping-projects-pair-jobs-if-not-exists <file-list> <chunk-size>

n=`wc -l < ${1}`
mod=${2:-100}

step=$(($mod/2))
first=0
last=$(($n-1))

pwd=`pwd`
mkdir -p $pwd/jobs/log
cd $pwd/jobs/log

for i in `seq $first $step $(($last-$step))` 
do
	range="$i-$(($i+3*$step-1))"
	range2="$(($i+$step))-$(($i+3*$step-1))"
	if [ ! -e "$pwd/$range2/rigid.txt" ]
        then
		echo "re-submitting range $range"
		qsub -cwd -pe batch 1 $pwd/jobs/align-overlapping-projects-pair-$range
	fi
done

cd $pwd