Making scripts more consistent by having check for system for juicer_tools path (a52e1760) · Commits · Chaos / chaos.juicer

SLURM/scripts/juicer_arrowhead.sh

+15 −0

Changes for SLURM/scripts/juicer_arrowhead.sh: 15 added lines, 0 removed lines.
Original line number	Diff line number	Diff line
		@@ -37,7 +37,22 @@ printHelpAndExit() {
		#set defaults
		genomeID="hg19"
		hic_file_path="$(pwd)/aligned/inter_30.hic"

		# Aiden Lab specific check
		isRice=$(hostname \| awk '{if ($1~/rice/){print 1}else {print 0}}')
		isBCM=$(hostname \| awk '{if ($1~/bcm/){print 1}else {print 0}}')
		isVoltron=0
		# Set default appropriately
		if [ $isRice -eq 1 ]
		then
		juicer_tools_path="/projects/ea14/juicer/scripts/juicer_tools"
		elif [ $isBCM -eq 1 ]
		then
		juicer_tools_path="/storage/aiden/juicer/scripts/juicer_tools"
		else
		isVoltron=1
		juicer_tools_path="/gpfs0/juicer/scripts/juicer_tools"
		fi

		while getopts "h:j:i:" opt; do
		case $opt in

+17 −0

Changes for SLURM/scripts/juicer_hiccups.sh: 17 added lines, 0 removed lines.
Original line number	Diff line number	Diff line
		@@ -37,8 +37,25 @@ printHelpAndExit() {
		#set defaults
		genomeID="hg19"
		hic_file_path="$(pwd)/aligned/inter_30.hic"

		# Aiden Lab specific check
		isRice=$(hostname \| awk '{if ($1~/rice/){print 1}else {print 0}}')
		isBCM=$(hostname \| awk '{if ($1~/bcm/){print 1}else {print 0}}')
		isVoltron=0
		# Set default appropriately
		if [ $isRice -eq 1 ]
		then
		juicer_tools_path="/projects/ea14/juicer/scripts/juicer_tools"
		bed_file_dir="/projects/ea14/juicer/references/motif"
		elif [ $isBCM -eq 1 ]
		then
		juicer_tools_path="/storage/aiden/juicer/scripts/juicer_tools"
		bed_file_dir="/storage/aiden/juicer/references/motif"
		else
		isVoltron=1
		juicer_tools_path="/gpfs0/juicer/scripts/juicer_tools"
		bed_file_dir="/gpfs0/juicer/references/motif"
		fi

		while getopts "h:g:j:i:m:" opt; do
		case $opt in

+17 −0

Changes for SLURM/scripts/juicer_postprocessing.sh: 17 added lines, 0 removed lines.
Original line number	Diff line number	Diff line
		@@ -39,8 +39,25 @@ printHelpAndExit() {
		#set defaults
		genomeID="hg19"
		hic_file_path="$(pwd)/aligned/inter_30.hic"

		# Aiden Lab specific check
		isRice=$(hostname \| awk '{if ($1~/rice/){print 1}else {print 0}}')
		isBCM=$(hostname \| awk '{if ($1~/bcm/){print 1}else {print 0}}')
		isVoltron=0
		# Set default appropriately
		if [ $isRice -eq 1 ]
		then
		juicer_tools_path="/projects/ea14/juicer/scripts/juicer_tools"
		bed_file_dir="/projects/ea14/juicer/references/motif"
		elif [ $isBCM -eq 1 ]
		then
		juicer_tools_path="/storage/aiden/juicer/scripts/juicer_tools"
		bed_file_dir="/storage/aiden/juicer/references/motif"
		else
		isVoltron=1
		juicer_tools_path="/gpfs0/juicer/scripts/juicer_tools"
		bed_file_dir="/gpfs0/juicer/references/motif"
		fi

		while getopts "h:g:j:i:m:" opt; do
		case $opt in