Merge pull request #40 from mzhibo/master (d6550a32) · Commits · Chaos / chaos.juicer

PBS/juicer.sh→PBS/scripts/juicer.sh

+7 −1

Changes for PBS/scripts/juicer.sh: 7 added lines, 1 removed line.
Original line number	Diff line number	Diff line
		@@ -452,6 +452,12 @@ SPLITMV
		# aligning read2, and merging the two. Keep track of merge names for final
		# merge. When merge jobs successfully finish, can launch final merge job.

		if [ -n "$threads" ] && [ -z "$skipsplit" ]
		then
		waitstring_alnwrp="#PBS -W depend=afterok:${jID_splitmv}"
		fi
		echo "waitstring_alnwrp is ${waitstring_alnwrp}"

		timestamp=$(date +"%s" \| cut -c 4-10)
		qsub <<ALIGNWRAP
		#PBS -S /bin/bash
		@@ -462,7 +468,7 @@ SPLITMV
		#PBS -o ${logdir}/${timestamp}_alnwrap_${groupname}.log
		#PBS -j oe
		#PBS -N AlnWrp${groupname}
		#PBS -W depend=afterok:${jID_splitmv}
		$waitstring_alnwrp
		${EMAIL}
		#PBS -m a
		for i in ${read1}

+0 −0

File moved.

+2 −2

Changes for PBS/scripts/postprocessing.sh: 2 added lines, 2 removed lines.
Original line number	Diff line number	Diff line
		@@ -26,7 +26,7 @@ if [ -z $postproc ]
		then
		waitstring4="#PBS -W depend=afterok:\${jID_hic30}"
		fi
		echo "waitstring4 is : ${waitstring4}"
		echo "waitstring4 is : \${waitstring4}"

		timestamp=\$(date +"%s" \| cut -c 4-10)
		qsub <<POSTPROCESS
		@@ -38,7 +38,7 @@ qsub <<POSTPROCESS
		#PBS -o ${logdir}/\${timestamp}_postproc_${groupname}.log
		#PBS -j oe
		#PBS -N PProc_${groupname}
		$waitstring4
		\$waitstring4

		date +"%Y-%m-%d %H:%M:%S"
		$load_java