Update mega.sh (b8cecf01) · Commits · Chaos / chaos.juicer

PBS/scripts/mega.sh

+9 −12

Changes for PBS/scripts/mega.sh: 9 added lines, 12 removed lines.
Original line number	Diff line number	Diff line
		@@ -48,8 +48,7 @@ juiceDir="/lustre1/mzhibo/hic/apps/juicer"
		# unique name for jobs in this run
		groupname="C$(date +"%s"\|cut -c 6-11)"

		#give an email to receive notification when a job exit with error
		EMAIL=""

		## Default options, overridden by command line arguments

		# top level directory, can also be set in options
		@@ -59,8 +58,6 @@ site="MboI"
		# genome ID, default to human, can also be set in options
		genomeID="hg19"

		#the resolution is optional, set only when you want resolution other than the default
		resolutions="1M,500K,100K,50K,10K,5K,3K,2K"
		## Read arguments
		usageHelp="Usage: ${0##*/} -g genomeID [-d topDir] [-s site] [-r resolutions] [-hx]"
		genomeHelp=" genomeID must be defined in the script, e.g. \"hg19\" or \"mm10\" (default \"$genomeID\")"
		@@ -235,11 +232,11 @@ jid5=$(qsub -o ${logdir}/hic0_${groupname}.log -j oe -q batch -M ${EMAIL} -m ae
		$load_java
		if [ -z "$exclude" ]
		then
		echo "Launching ${juiceDir}/scripts/juicer_tools pre -f ${site_file} -s ${outputdir}/inter.txt -g ${outputdir}/inter_hists.m -q 1 ${outputdir}/merged_nodups.txt ${outputdir}/inter.hic ${genomeID}"
		${juiceDir}/scripts/juicer_tools pre -f ${site_file} -s ${outputdir}/inter.txt -g ${outputdir}/inter_hists.m -q 1 ${outputdir}/merged_nodups.txt ${outputdir}/inter.hic ${genomeID}
		echo "Launching ${juiceDir}/scripts/juicer_tools pre ${resolutions} -f ${site_file} -s ${outputdir}/inter.txt -g ${outputdir}/inter_hists.m -q 1 ${outputdir}/merged_nodups.txt ${outputdir}/inter.hic ${genomeID}"
		${juiceDir}/scripts/juicer_tools pre ${resolutions} -f ${site_file} -s ${outputdir}/inter.txt -g ${outputdir}/inter_hists.m -q 1 ${outputdir}/merged_nodups.txt ${outputdir}/inter.hic ${genomeID}
		else
		echo "Launching ${juiceDir}/scripts/juicer_tools pre -s ${outputdir}/inter.txt -g ${outputdir}/inter_hists.m -q 1 ${outputdir}/merged_nodups.txt ${outputdir}/inter.hic ${genomeID}"
		${juiceDir}/scripts/juicer_tools pre -s ${outputdir}/inter.txt -g ${outputdir}/inter_hists.m -q 1 ${outputdir}/merged_nodups.txt ${outputdir}/inter.hic ${genomeID}
		echo "Launching ${juiceDir}/scripts/juicer_tools pre ${resolutions} -s ${outputdir}/inter.txt -g ${outputdir}/inter_hists.m -q 1 ${outputdir}/merged_nodups.txt ${outputdir}/inter.hic ${genomeID}"
		${juiceDir}/scripts/juicer_tools pre ${resolutions} -s ${outputdir}/inter.txt -g ${outputdir}/inter_hists.m -q 1 ${outputdir}/merged_nodups.txt ${outputdir}/inter.hic ${genomeID}
		fi
		HIC0
		)
		@@ -249,11 +246,11 @@ jid6=$(qsub -o ${logdir}/hic30_${groupname}.log -j oe -q batch -M ${EMAIL} -m ae
		$load_java
		if [ -z "${exclude}" ]
		then
		echo "Launching ${juiceDir}/scripts/juicer_tools pre -f ${site_file} -s ${outputdir}/inter_30.txt -g ${outputdir}/inter_30_hists.m -q 30 ${outputdir}/merged_nodups.txt ${outputdir}/inter_30.hic ${genomeID}"
		${juiceDir}/scripts/juicer_tools pre -f ${site_file} -s ${outputdir}/inter_30.txt -g ${outputdir}/inter_30_hists.m -q 30 ${outputdir}/merged_nodups.txt ${outputdir}/inter_30.hic ${genomeID}
		echo "Launching ${juiceDir}/scripts/juicer_tools pre ${resolutions} -f ${site_file} -s ${outputdir}/inter_30.txt -g ${outputdir}/inter_30_hists.m -q 30 ${outputdir}/merged_nodups.txt ${outputdir}/inter_30.hic ${genomeID}"
		${juiceDir}/scripts/juicer_tools pre ${resolutions} -f ${site_file} -s ${outputdir}/inter_30.txt -g ${outputdir}/inter_30_hists.m -q 30 ${outputdir}/merged_nodups.txt ${outputdir}/inter_30.hic ${genomeID}
		else
		echo "Launching ${juiceDir}/scripts/juicer_tools pre -s ${outputdir}/inter_30.txt -g ${outputdir}/inter_30_hists.m -q 30 ${outputdir}/merged_nodups.txt ${outputdir}/inter_30.hic ${genomeID}"
		${juiceDir}/scripts/juicer_tools pre -s ${outputdir}/inter_30.txt -g ${outputdir}/inter_30_hists.m -q 30 ${outputdir}/merged_nodups.txt ${outputdir}/inter_30.hic ${genomeID}
		echo "Launching ${juiceDir}/scripts/juicer_tools pre ${resolutions} -s ${outputdir}/inter_30.txt -g ${outputdir}/inter_30_hists.m -q 30 ${outputdir}/merged_nodups.txt ${outputdir}/inter_30.hic ${genomeID}"
		${juiceDir}/scripts/juicer_tools pre ${resolutions} -s ${outputdir}/inter_30.txt -g ${outputdir}/inter_30_hists.m -q 30 ${outputdir}/merged_nodups.txt ${outputdir}/inter_30.hic ${genomeID}
		fi
		HIC30
		)

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