minor changes to better align scripts (d940e9e0) · Commits · Chaos / chaos.juicer

AWS/scripts/countligations.sh

+1 −1

Changes for AWS/scripts/countligations.sh: 1 added line, 1 removed line.
Original line number	Diff line number	Diff line
		@@ -25,7 +25,7 @@
		#
		# Small helper script to count reads with ligation junction
		# Juicer version 1.5
		if [ "$ARG1" -eq 1 ]
		if [ "$usegzip" -eq 1 ]
		then
		num1=$(paste <(zcat $name1$ext) <(zcat $name2$ext) \| grep -c $ligation)
		num2=$(zcat ${name1}${ext} \| wc -l \| awk '{print $1}')

AWS/scripts/juicer.sh

+1 −1

Changes for AWS/scripts/juicer.sh: 1 added line, 1 removed line.
Original line number	Diff line number	Diff line
		@@ -456,7 +456,7 @@ SPLITMV
		#BSUB -W $queue_time
		#BSUB -o $topDir/lsf.out
		#BSUB -J "${groupname}${jname}_Count_Ligation"
		export ARG1=${usegzip};export name=${name}; export name1=${name1}; export name2=${name2}; export ext=${ext}; export ligation=${ligation}; ${juiceDir}/scripts/countligations.sh
		export usegzip=${usegzip}; export name=${name}; export name1=${name1}; export name2=${name2}; export ext=${ext}; export ligation=${ligation}; ${juiceDir}/scripts/countligations.sh
		CNTLIG

		# align read1 fastq

AWS/scripts/juicer_postprocessing.sh

+10 −10

Changes for AWS/scripts/juicer_postprocessing.sh: 10 added lines, 10 removed lines.
Original line number	Diff line number	Diff line
		@@ -56,19 +56,13 @@ done
		## Check that juicer_tools exists
		if [ ! -e "${juicer_tools_path}" ]; then
		echo "***! Can't find juicer tools in ${juicer_tools_path}";
		exit 100;
		exit 1
		fi

		## Check that hic file exists
		if [ ! -e "${hic_file_path}" ]; then
		echo "***! Can't find inter.hic in ${hic_file_path}";
		exit 100;
		fi

		## Check that bed folder exists
		if [ ! -e "${bed_file_dir}" ]; then
		echo "***! Can't find folder ${bed_file_dir}";
		exit 100;
		exit 1
		fi

		echo -e "${juicer_tools_path} is post-processing Hi-C for ${genomeID}\nData read from ${hic_file_path}.\nMotifs read from ${bed_file_dir}\n"
		@@ -76,7 +70,7 @@ echo -e "ARROWHEAD:\n"
		${juicer_tools_path} arrowhead ${hic_file_path} ${hic_file_path%.*}"_contact_domains.txt"
		if [ $? -ne 0 ]; then
		echo "***! Problem while running Arrowhead";
		exit 100
		exit 1
		fi
		echo -e "\nHiCCUPS:\n"
		if hash nvcc 2>/dev/null
		@@ -84,7 +78,7 @@ then
		${juicer_tools_path} hiccups ${hic_file_path} ${hic_file_path%.*}"_loops.txt"
		if [ $? -ne 0 ]; then
		echo "***! Problem while running HiCCUPS";
		exit 100
		exit 1
		fi
		else
		echo "GPUs are not installed so HiCCUPs cannot be run";
		@@ -94,8 +88,14 @@ if [ -f ${hic_file_path%.*}"_loops.txt" ]
		then
		echo -e "\nAPA:\n"
		${juicer_tools_path} apa ${hic_file_path} ${hic_file_path%.*}"_loops.txt" "apa_results"
		## Check that bed folder exists
		if [ ! -e "${bed_file_dir}" ]; then
		echo "***! Can't find folder ${bed_file_dir}";
		echo "***! Not running motif finder";
		else
		echo -e "\nMOTIF FINDER:\n"
		${juicer_tools_path} motifs ${genomeID} ${bed_file_dir} ${hic_file_path%.*}"_loops.txt"
		fi
		echo -e "\n(-: Feature annotation successfully completed (-:"
		else
		# if loop lists do not exist but Juicer Tools didn't return an error, likely

LSF/scripts/juicer_hiccups.sh

+1 −1

Changes for LSF/scripts/juicer_hiccups.sh: 1 added line, 1 removed line.
Original line number	Diff line number	Diff line
		@@ -84,7 +84,7 @@ then
		${juicer_tools_path} motifs ${genomeID} ${bed_file_dir} ${hic_file_path%.*}"_loops.txt"
		echo -e "\n(-: Feature annotation successfully completed (-:"
		else
		# if loop lists do not exist but Juicer Tools didn't return an error, likely
		# if loop lists do not exist but Juicer tools didn't return an error, likely
		# too sparse
		echo -e "\n(-: Postprocessing successfully completed, maps too sparse to annotate (-:"
		fi

UGER/scripts/countligations.sh

+1 −1

Changes for UGER/scripts/countligations.sh: 1 added line, 1 removed line.
Original line number	Diff line number	Diff line
		@@ -25,7 +25,7 @@
		#
		# Small helper script to count reads with ligation junction
		# Juicer version 1.5
		if [ "$ARG1" -eq 1 ]
		if [ "$usegzip" -eq 1 ]
		then
		num1=$(paste <(zcat $name1$ext) <(zcat $name2$ext) \| grep -c $ligation)
		num2=$(zcat ${name1}${ext} \| wc -l \| awk '{print $1}')

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