# HG changeset patch
# User davidvanzessen
# Date 1453795659 18000
# Node ID 65134a538c5a0154535350c8d57f17cd5bc6bcd2
# Parent  85566b336a722940f3b43293d1d65ff5f502aace
Uploaded

diff -r 85566b336a72 -r 65134a538c5a report_clonality/r_wrapper.sh
--- a/report_clonality/r_wrapper.sh	Tue Jan 26 03:01:48 2016 -0500
+++ b/report_clonality/r_wrapper.sh	Tue Jan 26 03:07:39 2016 -0500
@@ -57,7 +57,7 @@
 	
 	circos_file="$outputDir/${sample}_VJ_circos.txt"
 	echo -e -n "labels$(cat ${circos_file})" > ${circos_file}
-	cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/
+	cat "${circos_file}" | $CIRCOSTOOLS/circos-tools-0.20/tools/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/circos-tools-0.20/tools/tableviewer/bin/make-conf -dir $outputDir/circos/
 	#/home/galaxy/Downloads/circos-master/bin/circos -conf $outputDir/circos/circos.conf 2>&1
 	circos -conf $outputDir/circos/circos.conf 2>&1
 	mv $outputDir/circos/circos.png $outputDir/circosVJ_${sample}.png
@@ -66,14 +66,14 @@
 	if [[ "$useD" == "true" ]] ; then
 		circos_file="$outputDir/${sample}_VD_circos.txt"
 		echo -e -n "labels$(cat ${circos_file})" > ${circos_file}
-		cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/
-		/home/galaxy/Downloads/circos-master/bin/circos -conf $outputDir/circos/circos.conf 2>&1
+		cat "${circos_file}" | $CIRCOSTOOLS/circos-tools-0.20/tools/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/circos-tools-0.20/tools/tableviewer/bin/make-conf -dir $outputDir/circos/
+		circos -conf $outputDir/circos/circos.conf 2>&1
 		mv $outputDir/circos/circos.png $outputDir/circosVD_${sample}.png
 		
 		circos_file="$outputDir/${sample}_DJ_circos.txt"
 		echo -e -n "labels$(cat ${circos_file})" > ${circos_file}
-		cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/
-		/home/galaxy/Downloads/circos-master/bin/circos -conf $outputDir/circos/circos.conf 2>&1
+		cat "${circos_file}" | $CIRCOSTOOLS/circos-tools-0.20/tools/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/circos-tools-0.20/tools/tableviewer/bin/make-conf -dir $outputDir/circos/
+		circos -conf $outputDir/circos/circos.conf 2>&1
 		mv $outputDir/circos/circos.png $outputDir/circosDJ_${sample}.png
 		
 	fi