# HG changeset patch
# User davidvanzessen
# Date 1490705825 14400
# Node ID edf2d5882b775706e8ec8249d0005bc6cbee6dcd
# Parent  dc6c53a11d7d023c309b74be42c1e18884109d33
Uploaded

diff -r dc6c53a11d7d -r edf2d5882b77 report_clonality/r_wrapper.sh
--- a/report_clonality/r_wrapper.sh	Tue Mar 28 08:51:34 2017 -0400
+++ b/report_clonality/r_wrapper.sh	Tue Mar 28 08:57:05 2017 -0400
@@ -93,7 +93,7 @@
 	cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/
 	$CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1
 	mv $outputDir/circos/circos.png $outputDir/circosVJ_${sample}.png
-	mv $outputDir/circos/circos.pdf $outputDir/circosVJ_${sample}.pdf
+	mv $outputDir/circos/circos.svg $outputDir/circosVJ_${sample}.svg
 	
 	
 	if [[ "$useD" == "true" ]] ; then
@@ -102,14 +102,14 @@
 		cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/
 		$CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1
 		mv $outputDir/circos/circos.png $outputDir/circosVD_${sample}.png
-		mv $outputDir/circos/circos.pdf $outputDir/circosVD_${sample}.pdf
+		mv $outputDir/circos/circos.svg $outputDir/circosVD_${sample}.svg
 		
 		circos_file="$outputDir/${sample}_DJ_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/
 		$CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1
 		mv $outputDir/circos/circos.png $outputDir/circosDJ_${sample}.png
-		mv $outputDir/circos/circos.pdf $outputDir/circosDJ_${sample}.pdf
+		mv $outputDir/circos/circos.svg $outputDir/circosDJ_${sample}.svg
 	fi
 done
 echo "</title><script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $outputFile