made things more consistent

megadir=${topDir}"/mega"

outputdir=${megadir}"/aligned"

tmpdir=${megadir}"/HIC_tmp"

export TMPDIR=${megadir}"/HIC_tmp"

export TMPDIR=${tmpdir}

outfile=${megadir}/lsf.out

#output messages

outDir="$megadir/debug"

logdir="$megadir/debug"

touchfile1=${megadir}/touch1

fi

## Create output directory, used for reporting commands output

if [ ! -d "$outDir" ]; then

        mkdir "$outDir"

        chmod 777 "$outDir"

if [ ! -d "$logdir" ]; then

        mkdir "$logdir"

        chmod 777 "$logdir"

fi

## Arguments have been checked and directories created. Now begins

#SBATCH -t 1440

#SBATCH -c 1

#SBATCH --ntasks=1

#SBATCH -o $outDir/topstats-%j.out

#SBATCH -e $outDir/topstats-%j.err

#SBATCH -o $logdir/topstats-%j.out

#SBATCH -e $logdir/topstats-%j.err

#SBATCH -J "${groupname}_topstats"

export LC_COLLATE=C

if ! awk -f ${juiceDir}/scripts/makemega_addstats.awk ${inter_names} > ${outputdir}/inter.txt

#SBATCH -c 1

#SBATCH --ntasks=1

#SBATCH --mem-per-cpu=16384

#SBATCH -o $outDir/merge-%j.out

#SBATCH -e $outDir/merge-%j.err

#SBATCH -o $logdir/merge-%j.out

#SBATCH -e $logdir/merge-%j.err

#SBATCH -J "${groupname}_merge"

#SBATCH -d "${dependtopstats}"

if [ ! -f "${touchfile1}" ]

#SBATCH -t 1440

#SBATCH -c 1

#SBATCH --ntasks=1

#SBATCH -o $outDir/inter0-%j.out

#SBATCH -e $outDir/inter0-%j.err

#SBATCH -o $logdir/inter0-%j.out

#SBATCH -e $logdir/inter0-%j.err

#SBATCH -J "${groupname}_inter0"

#SBATCH -d "${dependmerge}"

if [ ! -f "${touchfile2}" ]

#SBATCH -t 1440

#SBATCH -c 1

#SBATCH --ntasks=1

#SBATCH -o $outDir/inter30-%j.out

#SBATCH -e $outDir/inter30-%j.err

#SBATCH -o $logdir/inter30-%j.out

#SBATCH -e $logdir/inter30-%j.err

#SBATCH -J "${groupname}_inter30"

#SBATCH -d "${dependmerge}"

if [ ! -f "${touchfile2}" ]

#SBATCH -t 1440

#SBATCH -c 1

#SBATCH --ntasks=1

#SBATCH -o $outDir/hic0-%j.out

#SBATCH -e $outDir/hic0-%j.err

#SBATCH -o $logdir/hic0-%j.out

#SBATCH -e $logdir/hic0-%j.err

#SBATCH -J "${groupname}_hic0"

#SBATCH -d "${dependinter0}"

#SBATCH --mem-per-cpu=32G

#SBATCH -t 1440

#SBATCH -c 1

#SBATCH --ntasks=1

#SBATCH -o $outDir/hic30-%j.out

#SBATCH -e $outDir/hic30-%j.err

#SBATCH -o $logdir/hic30-%j.out

#SBATCH -e $logdir/hic30-%j.err

#SBATCH -J "${groupname}_hic30"

#SBATCH -d "${dependinter30}"

#SBATCH --mem-per-cpu=32G

#SBATCH --ntasks=1

#SBATCH --mem-per-cpu=4G 

#SBATCH --gres=gpu:kepler:1

#SBATCH -o $outDir/hiccups-%j.out

#SBATCH -e $outDir/hiccups-%j.err

#SBATCH -o $logdir/hiccups-%j.out

#SBATCH -e $logdir/hiccups-%j.err

#SBATCH -J "${groupname}_hiccups"

#SBATCH -d "${dependhic30only}"

#source $usePath

touchfile8=${megadir}/touch8

# Create domain lists for MQ > 30

jid8=`sbatch <<- ARROWS | egrep -o -e "\b[0-9]+$"

jid8=`sbatch <<- ARROWHEAD | egrep -o -e "\b[0-9]+$"

#!/bin/bash -l

#SBATCH -p ${long_queue}

#SBATCH -t 1440

#SBATCH -c 2

#SBATCH --ntasks=1

#SBATCH --mem-per-cpu=4G 

#SBATCH -o $outDir/arrowhead-%j.out

#SBATCH -e $outDir/arrowhead-%j.err

#SBATCH -o $logdir/arrowhead-%j.out

#SBATCH -e $logdir/arrowhead-%j.err

#SBATCH -J "${groupname}_arrowhead"

#SBATCH -d "${dependhic30only}"

#source $usePath

   echo "***! HIC maps q=30 job failed."

   exit 100;

fi

${juiceDir}/scripts/juicer_arrows.sh -j ${juiceDir}/scripts/juicebox -i $outputdir/inter_30.hic

${juiceDir}/scripts/juicer_arrowhead.sh -j ${juiceDir}/scripts/juicebox -i $outputdir/inter_30.hic

touch $touchfile8

ARROWS`

ARROWHEAD`

dependarrows="${dependhic0}:$jid8"

dependarrowsonly="afterok:$jid8"

#SBATCH -t 100

#SBATCH -c 1

#SBATCH --ntasks=1

#SBATCH -o $outDir/done-%j.out

#SBATCH -e $outDir/done-%j.err

#SBATCH -o $logdir/done-%j.out

#SBATCH -e $logdir/done-%j.err

#SBATCH -J "${groupname}_done"

#SBATCH -d "${dependarrows}"