# HG changeset patch
# User davidvanzessen
# Date 1482159821 18000
# Node ID 5f5d29c5e711205e78ae79827d5d44251159837e
# Parent  607f176350bf9eb06a539bfd8041be5d8bf5ced9
Uploaded

diff -r 607f176350bf -r 5f5d29c5e711 report_clonality/r_wrapper.sh
--- a/report_clonality/r_wrapper.sh	Mon Dec 19 09:48:15 2016 -0500
+++ b/report_clonality/r_wrapper.sh	Mon Dec 19 10:03:41 2016 -0500
@@ -62,12 +62,19 @@
 if [ -d "$CIRCOSDIR" ]; then
 	USECIRCOS="yes"
 else
-	if [ -d "/home/galaxy/Anaconda3/bin" ]; then #hopefully temporary fix
+	if [ -d "/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/bin/" ]; then #hopefully temporary fix
 		USECIRCOS="yes"
 		CIRCOSTOOLS="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/circos-tools-0.21/tools"
 		CIRCOSDIR="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/bin/"
 	fi
+	
+	if [ -d "/home/galaxy/Anaconda3/bin" ]; then #hopefully temporary fix
+		USECIRCOS="yes"
+		CIRCOSTOOLS="/home/galaxy/circos/circos-tools-0.22/tools"
+		CIRCOSDIR="/home/galaxy/Anaconda3/bin"
+	fi
 fi
+
 echo "Using Circos: $USECIRCOS"
 sed -i "s%DATA_DIR%$outputDir/circos%" $outputDir/circos/circos.conf
 for sample in $samples; do #output the samples to a file and create the circos plots with the R script output