Merge pull request #128 from cErikson/master (3c6609e1) · Commits · Chaos / chaos.juicer

SLURM/scripts/juicer.sh

+7 −1

Changes for SLURM/scripts/juicer.sh: 7 added lines, 1 removed line.
Original line number	Diff line number	Diff line
		@@ -274,6 +274,11 @@ if [ ! -e "${refSeq}.bwt" ]; then
		exit 1;
		fi

		## Check if ligation is a unquoted regex, if so quote
		if [[ -n "$ligation" && $ligation =~ [\\|] && ! $ligation =~ [\"\'] ]]; then
		export ligation="'$ligation'"
		fi

		## Set ligation junction based on restriction enzyme
		if [ -z "$ligation" ]; then
		case $site in
		@@ -283,6 +288,7 @@ if [ -z "$ligation" ]; then
		MboI) ligation="GATCGATC";;
		NcoI) ligation="CCATGCATGG";;
		MboI+HindIII) ligation="'(GATCGATC\|AAGCTAGCTT)'";;
		Arima) ligation="'(GAATAATC\|GAATACTC\|GAATAGTC\|GAATATTC\|GAATGATC\|GACTAATC\|GACTACTC\|GACTAGTC\|GACTATTC\|GACTGATC\|GAGTAATC\|GAGTACTC\|GAGTAGTC\|GAGTATTC\|GAGTGATC\|GATCAATC\|GATCACTC\|GATCAGTC\|GATCATTC\|GATCGATC\|GATTAATC\|GATTACTC\|GATTAGTC\|GATTATTC\|GATTGATC)'";;
		none) ligation="XXXX";;
		*) ligation="XXXX"
		echo "$site not listed as recognized enzyme. Using $site_file as site file"
		@@ -725,7 +731,7 @@ ALGNR2`
		#SBATCH -e $debugdir/merge-%j.err
		#SBATCH --mem=50G
		#SBATCH -t $long_queue_time
		#SBATCH -c 32
		#SBATCH -c $threads
		#SBATCH --ntasks=1
		#SBATCH -d $dependalign
		#SBATCH -J "${groupname}_merge_${jname}"