Fixing bug in relaunch at final stage on AWS (44f5dd5c) · Commits · Chaos / chaos.juicer

AWS/scripts/juicebox

+2 −1

Original line number	Diff line number	Diff line
		@@ -20,4 +20,5 @@
		# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
		# THE SOFTWARE.
		#
		java -Djava.io.tmpdir=/opt/juicer/tmp -Djava.awt.headless=true -Djava.library.path=/opt/cuda-7.0/lib64 -Xmx32000m -Xms8000m -jar /opt/juicer/scripts/juicebox_tools.7.0.jar $*
		# Juicer 1.5
		java -Djava.io.tmpdir=/opt/juicer/tmp -Djava.awt.headless=true -Djava.library.path=`dirname $0`/lib64 -Xmx32000m -Xms8000m -jar `dirname $0`/juicebox_tools.7.0.jar $*
		No newline at end of file

AWS/scripts/juicer.sh

+5 −3

Original line number	Diff line number	Diff line
		@@ -768,6 +768,8 @@ then
		if [ -z $final ]
		then
		waitstring2="#BSUB -w \" done(${groupname}_osplit) \""
		execstring="bkill -J ${groupname}_clean2 "
		waitstring22="-w \"done(${groupname}_rmsplit) && done(${groupname}_osplit)\""
		fi
		## LSF users change queue below to $queue
		bsub <<- DOSTAT
		@@ -778,10 +780,10 @@ then
		${waitstring2}
		#BSUB -J "${groupname}_launch"
		echo "(-: Alignment and merge done, launching other jobs."
		bkill -J ${groupname}_clean2
		bsub -o $topDir/lsf.out -q $long_queue -W $long_queue_time -R "rusage[mem=16000]" -w "done(${groupname}_rmsplit) && done(${groupname}_osplit)" -J "${groupname}_stats" "df -h;_JAVA_OPTIONS=-Xmx16384m; export LC_ALL=en_US.UTF-8; echo -e 'Experiment description: $about' > $outputdir/inter.txt; ${juiceDir}/scripts/statistics.pl -s $site_file -l $ligation -o $outputdir/stats_dups.txt $outputdir/dups.txt; cat $splitdir/.res.txt \| awk -f ${juiceDir}/scripts/stats_sub.awk >> $outputdir/inter.txt; java -cp ${juiceDir}/scripts/ LibraryComplexity $outputdir inter.txt >> $outputdir/inter.txt; ${juiceDir}/scripts/statistics.pl -s $site_file -l $ligation -o $outputdir/inter.txt -q 1 $outputdir/merged_nodups.txt; cat $splitdir/_abnorm.sam > $outputdir/abnormal.sam; cat $splitdir/*_unmapped.sam > $outputdir/unmapped.sam; awk -f ${juiceDir}/scripts/collisions.awk $outputdir/abnormal.sam > $outputdir/collisions.txt"
		$execstring
		bsub -o $topDir/lsf.out -q $long_queue -W $long_queue_time -R "rusage[mem=16000]" $waitstring22 -J "${groupname}_stats" "df -h;_JAVA_OPTIONS=-Xmx16384m; export LC_ALL=en_US.UTF-8; echo -e 'Experiment description: $about' > $outputdir/inter.txt; ${juiceDir}/scripts/statistics.pl -s $site_file -l $ligation -o $outputdir/stats_dups.txt $outputdir/dups.txt; cat $splitdir/.res.txt \| awk -f ${juiceDir}/scripts/stats_sub.awk >> $outputdir/inter.txt; java -cp ${juiceDir}/scripts/ LibraryComplexity $outputdir inter.txt >> $outputdir/inter.txt; ${juiceDir}/scripts/statistics.pl -s $site_file -l $ligation -o $outputdir/inter.txt -q 1 $outputdir/merged_nodups.txt; cat $splitdir/_abnorm.sam > $outputdir/abnormal.sam; cat $splitdir/*_unmapped.sam > $outputdir/unmapped.sam; awk -f ${juiceDir}/scripts/collisions.awk $outputdir/abnormal.sam > $outputdir/collisions.txt"
		bsub -o $topDir/lsf.out -q $long_queue -W $long_queue_time -R "rusage[mem=16000]" -w "done(${groupname}_stats)" -J "${groupname}_hic" "df -h;export _JAVA_OPTIONS=-Xmx16384m; if [ -n \"$nofrag\" ]; then ${juiceDir}/scripts/juicebox pre -s $outputdir/inter.txt -g $outputdir/inter_hists.m -q 1 $outputdir/merged_nodups.txt $outputdir/inter.hic $genomePath; else ${juiceDir}/scripts/juicebox pre -f $site_file -s $outputdir/inter.txt -g $outputdir/inter_hists.m -q 1 $outputdir/merged_nodups.txt $outputdir/inter.hic $genomePath; fi ;"
		bsub -o $topDir/lsf.out -q $long_queue -W $long_queue_time -R "rusage[mem=16000]" -w "done(${groupname}_rmsplit) && done(${groupname}_osplit)" -J "${groupname}_hic30" "df -h;export _JAVA_OPTIONS=-Xmx16384m; export LC_ALL=en_US.UTF-8; echo -e 'Experiment description: $about' > $outputdir/inter_30.txt; cat $splitdir/*.res.txt \| awk -f ${juiceDir}/scripts/stats_sub.awk >> $outputdir/inter_30.txt; java -cp ${juiceDir}/scripts/ LibraryComplexity $outputdir inter_30.txt >> $outputdir/inter_30.txt; ${juiceDir}/scripts/statistics.pl -s $site_file -l $ligation -o $outputdir/inter_30.txt -q 30 $outputdir/merged_nodups.txt; export _JAVA_OPTIONS=-Xmx8192m; if [ -n \"$nofrag\" ]; then ${juiceDir}/scripts/juicebox pre -s $outputdir/inter_30.txt -g $outputdir/inter_30_hists.m -q 30 $outputdir/merged_nodups.txt $outputdir/inter_30.hic $genomePath; else ${juiceDir}/scripts/juicebox 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 $genomePath; fi"
		bsub -o $topDir/lsf.out -q $long_queue -W $long_queue_time -R "rusage[mem=16000]" $waitstring22 -J "${groupname}_hic30" "df -h;export _JAVA_OPTIONS=-Xmx16384m; export LC_ALL=en_US.UTF-8; echo -e 'Experiment description: $about' > $outputdir/inter_30.txt; cat $splitdir/*.res.txt \| awk -f ${juiceDir}/scripts/stats_sub.awk >> $outputdir/inter_30.txt; java -cp ${juiceDir}/scripts/ LibraryComplexity $outputdir inter_30.txt >> $outputdir/inter_30.txt; ${juiceDir}/scripts/statistics.pl -s $site_file -l $ligation -o $outputdir/inter_30.txt -q 30 $outputdir/merged_nodups.txt; export _JAVA_OPTIONS=-Xmx8192m; if [ -n \"$nofrag\" ]; then ${juiceDir}/scripts/juicebox pre -s $outputdir/inter_30.txt -g $outputdir/inter_30_hists.m -q 30 $outputdir/merged_nodups.txt $outputdir/inter_30.hic $genomePath; else ${juiceDir}/scripts/juicebox 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 $genomePath; fi"
		DOSTAT
		waitstring3="#BSUB -w \" done(${groupname}_launch) \""
		waitstring4="-w \"done(${groupname}_hic30)\""

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