Change juicebox to juicer_tools (1aefcb93) · Commits · Chaos / chaos.juicer

CPU/juicer.sh

+5 −5

Changes for CPU/juicer.sh: 5 added lines, 5 removed lines.
Original line number	Diff line number	Diff line
		@@ -499,9 +499,9 @@ then
		awk -f ${juiceDir}/scripts/common/collisions.awk $outputdir/abnormal.sam > $outputdir/collisions.txt
		if [ -n "$nofrag" ]
		then
		${juiceDir}/scripts/common/juicebox pre -s $outputdir/inter.txt -g $outputdir/inter_hists.m -q 1 $outputdir/merged_nodups.txt $outputdir/inter.hic $genomePath
		${juiceDir}/scripts/common/juicer_tools pre -s $outputdir/inter.txt -g $outputdir/inter_hists.m -q 1 $outputdir/merged_nodups.txt $outputdir/inter.hic $genomePath
		else
		${juiceDir}/scripts/common/juicebox pre -f $site_file -s $outputdir/inter.txt -g $outputdir/inter_hists.m -q 1 $outputdir/merged_nodups.txt $outputdir/inter.hic $genomePath
		${juiceDir}/scripts/common/juicer_tools pre -f $site_file -s $outputdir/inter.txt -g $outputdir/inter_hists.m -q 1 $outputdir/merged_nodups.txt $outputdir/inter.hic $genomePath
		fi
		echo -e "Experiment description: $about" > $outputdir/inter_30.txt
		cat $splitdir/*.res.txt \| awk -f ${juiceDir}/scripts/common/stats_sub.awk >> $outputdir/inter_30.txt
		@@ -509,13 +509,13 @@ then
		${juiceDir}/scripts/common/statistics.pl -s $site_file -l $ligation -o $outputdir/inter_30.txt -q 30 $outputdir/merged_nodups.txt
		if [ -n "$nofrag" ]
		then
		${juiceDir}/scripts/common/juicebox pre -s $outputdir/inter_30.txt -g $outputdir/inter_30_hists.m -q 30 $outputdir/merged_nodups.txt $outputdir/inter_30.hic $genomePath
		${juiceDir}/scripts/common/juicer_tools pre -s $outputdir/inter_30.txt -g $outputdir/inter_30_hists.m -q 30 $outputdir/merged_nodups.txt $outputdir/inter_30.hic $genomePath
		else
		${juiceDir}/scripts/common/juicebox pre -f $site_file -s $outputdir/inter_30.txt -g $outputdir/inter_30_hists.m -q 30 $outputdir/merged_nodups.txt $outputdir/inter_30.hic $genomePath
		${juiceDir}/scripts/common/juicer_tools pre -f $site_file -s $outputdir/inter_30.txt -g $outputdir/inter_30_hists.m -q 30 $outputdir/merged_nodups.txt $outputdir/inter_30.hic $genomePath
		fi
		fi
		# POSTPROCESSING
		${juiceDir}/scripts/common/juicer_postprocessing.sh -j ${juiceDir}/scripts/common/juicebox -i ${outputdir}/inter_30.hic -m ${juiceDir}/references/motif -g ${genomeID}
		${juiceDir}/scripts/common/juicer_postprocessing.sh -j ${juiceDir}/scripts/common/juicer_tools -i ${outputdir}/inter_30.hic -m ${juiceDir}/references/motif -g ${genomeID}
		fi
		#CHECK THAT PIPELINE WAS SUCCESSFUL
		source ${juiceDir}/scripts/common/check.sh

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