# HG changeset patch
# User jeremie
# Date 1403255125 14400
# Node ID 7b71d14e0f785aa4625458437c4a5507f7507196
# Parent  14facf79b652a607293450c2b402d2f0adc59c58
Uploaded

diff -r 14facf79b652 -r 7b71d14e0f78 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Jun 20 04:52:48 2014 -0400
+++ b/tool_dependencies.xml	Fri Jun 20 05:05:25 2014 -0400
@@ -18,10 +18,19 @@
 				</action>
 				<action type="shell_command">unzip pindel-master.zip -d pindel</action>
 				<action type="shell_command">cd master</action> -->
-				<action type="shell_command">sed '50d' Makefile</action>
+				<!-- <action type="shell_command">sed '50d' Makefile</action> -->
 				<!-- <action type="shell_command">make Makefile.local</action> -->
+				<action type="shell_command">
+				echo "SAMTOOLS=
+				THREADS=
+				COLOUSINGBD15_TIME=60
+				COLOWOBD15_TIME=80
+				SIM1CHRVS20305_TIME=60" >> Makefile.local
+				</action>
 				<action type="shell_command">make SAMTOOLS=~/samtools THREADS=2</action>
 				<!-- <action type="shell_command">./INSTALL ~/samtools</action>  -->
+				
+				
 				<action type="move_file">
 					<source>pindel</source>
 					<destination>$INSTALL_DIR/</destination>