Mercurial > repos > davidvanzessen > argalaxy_tools

diff report_clonality/r_wrapper.sh @ 2:4f8a1d121384 draft

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Uploaded
author davidvanzessen
date Mon, 05 Sep 2016 11:15:22 -0400
parents 90a05ff900db
children beaa487ecf43
line wrap: on
line diff
--- a/report_clonality/r_wrapper.sh	Mon Sep 05 04:46:06 2016 -0400
+++ b/report_clonality/r_wrapper.sh	Mon Sep 05 11:15:22 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