Changed shortread check from -v to -n, problem for LSF users otherwise (52a9c8d4) · Commits · Chaos / chaos.juicer

AWS/scripts/juicer.sh

+4 −4

Original line number	Diff line number	Diff line
		@@ -461,7 +461,7 @@ SPLITMV
		CNTLIG

		# align read1 fastq
		if [ -v shortread ] \|\| [ "$shortreadend" -eq 1 ]
		if [ -n "$shortread" ] \|\| [ "$shortreadend" -eq 1 ]
		then
		alloc_mem=16000
		else
		@@ -477,7 +477,7 @@ CNTLIG
		#BSUB -R "rusage[mem=$alloc_mem]"
		#BSUB -J "${groupname}_align1${jname}"
		# Align read1
		if [ -v shortread ] \|\| [ "$shortreadend" -eq 1 ]
		if [ -n "$shortread" ] \|\| [ "$shortreadend" -eq 1 ]
		then
		echo 'Running command bwa aln -q 15 $refSeq $name1$ext > $name1$ext.sai && bwa samse $refSeq $name1$ext.sai $name1$ext > $name1$ext.sam'
		bwa aln -q 15 $refSeq $name1$ext > $name1$ext.sai && bwa samse $refSeq $name1$ext.sai $name1$ext > $name1$ext.sam
		@@ -502,7 +502,7 @@ CNTLIG
		ALGNR1

		# align read2 fastq
		if [ -v shortread ] \|\| [ "$shortreadend" -eq 2 ]
		if [ -n "$shortread" ] \|\| [ "$shortreadend" -eq 2 ]
		then
		alloc_mem=16000
		else
		@@ -518,7 +518,7 @@ ALGNR1
		#BSUB -R "rusage[mem=$alloc_mem]"
		#BSUB -J "${groupname}_align2${jname}"
		# Align read2
		if [ -v shortread ] \|\| [ $shortreadend -eq 2 ]
		if [ -n "$shortread" ] \|\| [ "$shortreadend" -eq 2 ]
		then
		echo 'Running command bwa aln -q 15 $refSeq $name2$ext > $name2$ext.sai && bwa samse $refSeq $name2$ext.sai $name2$ext > $name2$ext.sam '
		bwa aln -q 15 $refSeq $name2$ext > $name2$ext.sai && bwa samse $refSeq $name2$ext.sai $name2$ext > $name2$ext.sam