diff report_clonality/r_wrapper.sh @ 46:fee06348bfad draft

Uploaded

--- a/report_clonality/r_wrapper.sh	Wed Jan 27 05:35:55 2016 -0500
+++ b/report_clonality/r_wrapper.sh	Wed Jan 27 08:39:16 2016 -0500
@@ -57,18 +57,18 @@
 if [ -d "$CIRCOSDIR" ]; then
 	USECIRCOS="yes"
 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
 	echo " $sample" >> $outputFile
 	
-	if [[ "$USECIRCOS" == "no" ]]; then
+	if [[ "$USECIRCOS" != "yes" ]]; then
 		continue
 	fi
 	
 	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
 	$CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1
 	mv $outputDir/circos/circos.png $outputDir/circosVJ_${sample}.png
 	
@@ -127,7 +127,7 @@
 
 #circos
 
-if [[ "$USECIRCOS" == "no" ]]; then
+if [[ "$USECIRCOS" == "yes" ]]; then
 
 	echo "<div class='tabbertab' title='Circos'><div class='tabber'>" >> $outputFile
 	for sample in $samples; do