# HG changeset patch
# User davidvanzessen
# Date 1453795097 18000
# Node ID a2fdcf1a2e50ead1635664304810f09896ecf6b6
# Parent  2e0a7c35082ef86c77518c2b9046c90a0182b9ab
Uploaded

diff -r 2e0a7c35082e -r a2fdcf1a2e50 report_clonality/r_wrapper.sh
--- a/report_clonality/r_wrapper.sh	Fri Jan 22 10:54:01 2016 -0500
+++ b/report_clonality/r_wrapper.sh	Tue Jan 26 02:58:17 2016 -0500
@@ -58,7 +58,8 @@
 	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/
-	/home/galaxy/Downloads/circos-master/bin/circos -conf $outputDir/circos/circos.conf 2>&1
+	#/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