Mercurial > repos > davidvanzessen > argalaxy_tools

changeset 12:5f5d29c5e711 draft

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Uploaded
author davidvanzessen
date Mon, 19 Dec 2016 10:03:41 -0500
parents 607f176350bf
children d3ebaa2d2fe0
files report_clonality/r_wrapper.sh
diffstat 1 files changed, 8 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- 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