# HG changeset patch
# User davidvanzessen
# Date 1473065166 14400
# Node ID 90a05ff900dbf5de04a4e5ec32958d145e87b17d
# Parent  afe85eb6572e4700cbf4ed73ce5f7dd620a6f3d4
Uploaded

diff -r afe85eb6572e -r 90a05ff900db report_clonality/RScript.r
--- a/report_clonality/RScript.r	Mon Aug 29 05:41:20 2016 -0400
+++ b/report_clonality/RScript.r	Mon Sep 05 04:46:06 2016 -0400
@@ -115,6 +115,9 @@
   clonalityFrame = clonalityFrame[!duplicated(clonalityFrame$clonality_clonaltype), ]
 }
 
+print("SAMPLE TABLE:")
+print(table(PRODF$Sample))
+
 prod.unique.sample.count = data.frame(data.table(PRODF)[, list(Productive_unique=.N), by=c("Sample")])
 prod.unique.rep.count = data.frame(data.table(PRODF)[, list(Productive_unique=.N), by=c("Sample", "Replicate")])
 
diff -r afe85eb6572e -r 90a05ff900db report_clonality/circos/LTe50046.ttf
Binary file report_clonality/circos/LTe50046.ttf has changed
diff -r afe85eb6572e -r 90a05ff900db report_clonality/circos/LTe50048.ttf
Binary file report_clonality/circos/LTe50048.ttf has changed
diff -r afe85eb6572e -r 90a05ff900db report_clonality/circos/LTe50050.ttf
Binary file report_clonality/circos/LTe50050.ttf has changed
diff -r afe85eb6572e -r 90a05ff900db report_clonality/circos/LTe50054.ttf
Binary file report_clonality/circos/LTe50054.ttf has changed
diff -r afe85eb6572e -r 90a05ff900db report_clonality/circos/circos.tar.gz
Binary file report_clonality/circos/circos.tar.gz has changed
diff -r afe85eb6572e -r 90a05ff900db report_clonality/circos/pragmata.ttf
Binary file report_clonality/circos/pragmata.ttf has changed
diff -r afe85eb6572e -r 90a05ff900db report_clonality/circos/wingding.ttf
Binary file report_clonality/circos/wingding.ttf has changed
diff -r afe85eb6572e -r 90a05ff900db report_clonality/r_wrapper.sh
--- a/report_clonality/r_wrapper.sh	Mon Aug 29 05:41:20 2016 -0400
+++ b/report_clonality/r_wrapper.sh	Mon Sep 05 04:46:06 2016 -0400
@@ -54,6 +54,10 @@
 cp $dir/circos/* $outputDir/circos/
 CIRCOSTOOLS="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/circos-tools-0.21/tools"
 CIRCOSDIR="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/bin/"
+
+CIRCOSTOOLS="/home/galaxy/circos/circos-tools-0.22/tools"
+CIRCOSDIR="/home/galaxy/Anaconda3/bin"
+
 USECIRCOS="no"
 if [ -d "$CIRCOSDIR" ]; then
 	USECIRCOS="yes"