create-run-resetBox-jobs

#!/bin/bash

# Resets the  
#
# Call:
#       ./create-run-resetBox-jobs <file-list> [<chunk-size> <export-dir> <project-base-dir> <num-jobs>]
# Defaults:
#   chunks-size:        100
#   export-dir:         $PWD
#   project-base-dir:   $PWD
#   num-jobs            20

if [ $# -lt 2 ]; then
    echo "Usage: $0 <file-list> [<chunk-size=100> <export-dir=$PWD> <project-base-dir=$PWD> <numJobs=20>]"
    exit 1
fi

pwd=`pwd`

n=`wc -l < ${1}`
mod=${2:-100}
exportDir="${3:-$PWD}"
projectBaseDir="${4:-$PWD}"
numJobs="${5:-20}"

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

numTasks=$[$n/$mod]
numTasks=$[2*$numTasks]
tasksPerJob=$((numTasks / numJobs))

echo "numJobs $numJobs"
echo "numTasks $numTasks"
echo "tasks per job: $tasksPerJob"

j=1
k=0

mkdir -p jobs

job="jobs/resetBox-$k"
echo "#!/bin/bash" > $job

#for i in `seq $first $step $(($last-3*$step))` 
for i in `seq $first $step $(($last-$step))` 
do

	if [ $j -ge $tasksPerJob ]; then
	   	chmod a+x $job # make the previous job executable
        # submit the job
        qsub -cwd -pe batch 1 $job

		j=0	
		((k++))
		job="jobs/resetBox-$k"
		echo "#!/bin/bash" > $job
	fi

	range1="$i-$(($i+2*$step-1))"
    echo $range1

	echo "${HOME}/bin/xvfb-run -a ${HOME}/packages/Fiji.app/ImageJ-linux64 -Xms10g -Xmx10g -Ddir=$projectBaseDir/$range1 -- --no-splash $projectBaseDir/reset-project-bounding-boxes.bsh" >> $job

	((j++))
done

chmod a+x $job # make the last job executable
qsub -cwd -pe batch 1 $job
cd $pwd