UGER mega.sh changes. Changed queue to be parameter, updated the memory flag (a7f78d5c) · Commits · Chaos / chaos.juicer

UGER/scripts/mega.sh

+5 −5

Changes for UGER/scripts/mega.sh: 5 added lines, 5 removed lines.
Original line number	Diff line number	Diff line
		@@ -203,7 +203,7 @@ TOPSTATS`

		touchfile2=${megadir}/touch2
		# Merge all merged_nodups.txt files found under current dir
		jid2=`qsub -terse -o ${logdir}/merge.out -e ${logdir}/merge.err -q ${queue} -r y -N ${groupname}_merge -l m_mem_free=16g -hold_jid ${groupname}_topstats <<- MRGSRT
		jid2=`qsub -terse -o ${logdir}/merge.out -e ${logdir}/merge.err -q ${queue} -r y -N ${groupname}_merge -l h_vmem=16g -hold_jid ${groupname}_topstats <<- MRGSRT
		if [ -n "$gzipped" ]
		then
		# This code didn't work, doesn't sort appropriately unfortunately.
		@@ -269,7 +269,7 @@ holdjobs3="-hold_jid ${groupname}_inter30";
		touchfile5=${megadir}/touch5

		# Create HIC maps file for MQ > 0
		jid5=`qsub -terse -o ${logdir}/hic0.out -e ${logdir}/hic0.err -q ${queue} -r y -N ${groupname}_hic0 -l m_mem_free=16g $holdjobs2 <<- HIC0
		jid5=`qsub -terse -o ${logdir}/hic0.out -e ${logdir}/hic0.err -q ${queue} -r y -N ${groupname}_hic0 -l h_vmem=16g $holdjobs2 <<- HIC0
		source $usePath
		$load_java
		if [ ! -f "${touchfile3}" ]
		@@ -296,7 +296,7 @@ HIC0`

		touchfile6=${megadir}/touch6
		# Create HIC maps file for MQ > 30
		jid6=`qsub -terse -o ${logdir}/hic30.out -e ${logdir}/hic30.err -q ${queue} -r y -N ${groupname}_hic30 -l m_mem_free=16g $holdjobs3 <<- HIC30
		jid6=`qsub -terse -o ${logdir}/hic30.out -e ${logdir}/hic30.err -q ${queue} -r y -N ${groupname}_hic30 -l h_vmem=16g $holdjobs3 <<- HIC30
		source $usePath
		$load_java
		if [ ! -f "${touchfile4}" ]
		@@ -322,7 +322,7 @@ fi
		HIC30`

		touchfile7=${megadir}/touch7
		jid7=`qsub -terse -o ${logdir}/hiccups.out -e ${logdir}/hiccups.err -q ${queue} -r y -N ${groupname}_hiccups -l m_mem_free=16g -hold_jid ${groupname}_hic30 <<- HICCUPS
		jid7=`qsub -terse -o ${logdir}/hiccups.out -e ${logdir}/hiccups.err -q ${queue} -r y -N ${groupname}_hiccups -l h_vmem=16g -hold_jid ${groupname}_hic30 <<- HICCUPS
		source $usePath;
		$load_java;
		export _JAVA_OPTIONS=-Xmx16384m;
		@@ -337,7 +337,7 @@ touch $touchfile7
		HICCUPS`

		touchfile8=${megadir}/touch8
		jid8=`qsub -terse -o ${logdir}/arrowhead.out -e ${logdir}/arrowhead.err -q ${queue} -r y -N ${groupname}_arrowhead -l m_mem_free=4g -hold_jid ${groupname}_hic30 <<- ARROWHEAD
		jid8=`qsub -terse -o ${logdir}/arrowhead.out -e ${logdir}/arrowhead.err -q ${queue} -r y -N ${groupname}_arrowhead -l h_vmem=4g -hold_jid ${groupname}_hic30 <<- ARROWHEAD
		source $usePath;
		$load_java;
		export _JAVA_OPTIONS=-Xmx16384m;

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