Fixed HIC_tmp hardcoding (d3ee11b5) · Commits · Chaos / chaos.juicer

SLURM/scripts/juicer.sh

+2 −2

Changes for SLURM/scripts/juicer.sh: 2 added lines, 2 removed lines.
Original line number	Diff line number	Diff line
		@@ -858,7 +858,7 @@ then

		if [ $isRice -eq 1 ]
		then
		if ! /work/ea14/olga-scripts/useful-small-scripts/sort --parallel=48 -S8G -T HIC_tmp -m -k2,2d -k6,6d -k4,4n -k8,8n -k1,1n -k5,5n -k3,3n $splitdir/*.sort.txt > $outputdir/merged_sort.txt
		if ! /work/ea14/olga-scripts/useful-small-scripts/sort --parallel=48 -S8G -T ${tmpdir} -m -k2,2d -k6,6d -k4,4n -k8,8n -k1,1n -k5,5n -k3,3n $splitdir/*.sort.txt > $outputdir/merged_sort.txt
		then
		echo "***! Some problems occurred somewhere in creating sorted align files."
		touch $errorfile
		@@ -867,7 +867,7 @@ then
		echo "(-: Finished sorting all sorted files into a single merge."
		fi
		else
		if ! sort --parallel=48 -S8G -T HIC_tmp -m -k2,2d -k6,6d -k4,4n -k8,8n -k1,1n -k5,5n -k3,3n $splitdir/*.sort.txt > $outputdir/merged_sort.txt
		if ! sort --parallel=48 -S8G -T ${tmpdir} -m -k2,2d -k6,6d -k4,4n -k8,8n -k1,1n -k5,5n -k3,3n $splitdir/*.sort.txt > $outputdir/merged_sort.txt
		then
		echo "***! Some problems occurred somewhere in creating sorted align files."
		touch $errorfile