Mercurial > repos > davidvanzessen > argalaxy_tools

diff report_clonality/r_wrapper.sh @ 75:899ca5c9601f draft default tip

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author davidvanzessen
date Mon, 05 Sep 2016 10:59:47 -0400
parents 08254c202db7
children
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--- a/report_clonality/r_wrapper.sh	Mon Sep 05 03:57:24 2016 -0400
+++ b/report_clonality/r_wrapper.sh	Mon Sep 05 10:59:47 2016 -0400
@@ -52,15 +52,21 @@
 
 mkdir $outputDir/circos
 cp $dir/circos/* $outputDir/circos/
-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/"
+#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/"
 
-CIRCOSTOOLS="/home/galaxy/circos/circos-tools-0.22/tools"
-CIRCOSDIR="/home/galaxy/Anaconda3/bin"
+#CIRCOSTOOLS="/home/galaxy/circos/circos-tools-0.22/tools"
+#CIRCOSDIR="/home/galaxy/Anaconda3/bin"
 
 USECIRCOS="no"
 if [ -d "$CIRCOSDIR" ]; then
 	USECIRCOS="yes"
+else
+	if [ -d "/home/galaxy/Anaconda3/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
 fi
 echo "Using Circos: $USECIRCOS"
 sed -i "s%DATA_DIR%$outputDir/circos%" $outputDir/circos/circos.conf