# HG changeset patch
# User jeremie
# Date 1403274506 14400
# Node ID 47817c9684221b227e334cd47598074fd003381d
# Parent  88444ff7009fa214fb6e923f74f8ca6ddba99ccf
Uploaded

diff -r 88444ff7009f -r 47817c968422 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Jun 20 08:59:35 2014 -0400
+++ b/tool_dependencies.xml	Fri Jun 20 10:28:26 2014 -0400
@@ -9,6 +9,12 @@
 				<!-- <action type="shell_command">git clone https://github.com/genome/pindel.git pindel</action> -->
 				<action type="download_by_url" target_filename="pindel-master.zip">https://github.com/genome/pindel/archive/master.zip</action>
 				<action type="shell_command">ls ..</action>
+				<action type="shell_command">
+					echo "$samtools
+					samtools
+					$PATH
+					$INSTALL_DIR"
+				</action>
 				<!-- <action type="shell_command">ls</action> -->
 				<!-- <action type="move_directory_files">
 					<source_directory>.</source_directory>
@@ -25,7 +31,7 @@
 				COLOWOBD15_TIME=80
 				SIM1CHRVS20305_TIME=60" > Makefile.local
 				</action>
-				<action type="shell_command">make SAMTOOLS=~/samtools THREADS=2</action>
+				<action type="shell_command">make SAMTOOLS=$samtools THREADS=2</action>
 				<action type="move_file">
 					<source>pindel</source>
 					<destination>$INSTALL_DIR/</destination>