Some bug fixes in SLURM and with CPU (3ccb4742) · Commits · Chaos / chaos.juicer

CPU/juicer.sh

+3 −3

Original line number	Diff line number	Diff line
		@@ -320,10 +320,10 @@ fi

		# Get version numbers of all software
		echo -ne "Juicer version $juicer_version;" >> $headfile
		bwa 2>&1 \| awk '\$1=="Version:"{printf(" BWA %s; ", \$2)}' >> $headfile
		bwa 2>&1 \| awk '$1=="Version:"{printf(" BWA %s; ", $2)}' >> $headfile
		echo -ne "$threads threads; " >> $headfile
		java -version 2>&1 \| awk 'NR==1{printf("%s; ", \$0);}' >> $headfile
		${juiceDir}/scripts/juicer_tools -V 2>&1 \| awk '\$1=="Juicer" && \$2=="Tools"{printf("%s; ", \$0);}' >> $headfile
		java -version 2>&1 \| awk 'NR==1{printf("%s; ", $0);}' >> $headfile
		${juiceDir}/scripts/juicer_tools -V 2>&1 \| awk '$1=="Juicer" && $2=="Tools"{printf("%s; ", $0);}' >> $headfile
		echo "$0 $@" >> $headfile

		## ALIGN FASTQ AS SINGLE END, SORT BY READNAME, HANDLE CHIMERIC READS

+3 −2

Original line number	Diff line number	Diff line
		@@ -100,9 +100,9 @@ then
		long_queue_time="3600"
		else
		isVoltron=1

		export PATH=/gpfs0/biobuild/biobuilds-2016.11/bin:$PATH
		unset MALLOC_ARENA_MAX
		load_gpu="CUDA_VISIBLE_DEVICES=0,1,2,3"
		# Juicer directory, contains scripts/, references/, and restriction_sites/
		# can also be set in options via -D
		juiceDir="/gpfs0/juicer/"
		@@ -1023,6 +1023,7 @@ DUPCHECK`
		echo "***! Found errorfile. Exiting."
		exit 1
		fi
		${load_java}
		export IBM_JAVA_OPTIONS="-Xmx16384m -Xgcthreads1"
		tail -n1 $headfile \| awk '{printf"%-1000s\n", \\\$0}' > $outputdir/inter.txt