# HG changeset patch
# User yhoogstrate
# Date 1387273965 18000
# Node ID ede8c645ed2234dfd15a47934d3c7e6ffc2e8887
# Parent  d0cd5668ec6becf585b8e9f1d66620b208a435e0
Uploaded

diff -r d0cd5668ec6b -r ede8c645ed22 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Dec 17 04:41:18 2013 -0500
+++ b/tool_dependencies.xml	Tue Dec 17 04:52:45 2013 -0500
@@ -3,9 +3,9 @@
 	<package name="samtools-mpileup-parallel" version="1.0.19">
 		<install version="1.0">
 			<actions>
-				<action type="shell_command">svn checkout https://github.com/mydatascience/parallel-mpileup/trunk samtools-mpileup-parallel &amp;&amp; cd samtools-mpileup-parallel &amp;&amp; cd $(ls |grep samtools-) &amp;&amp; make &amp;&amp; cp samtools ../samtools-mpileup-parallel &amp;&amp; ls -als &amp;&amp; cd .. &amp;&amp; ls -als</action>
+				<action type="shell_command">svn checkout https://github.com/mydatascience/parallel-mpileup/trunk samtools-mpileup-parallel &amp;&amp; cd samtools-mpileup-parallel &amp;&amp; cd $(ls |grep samtools-) &amp;&amp; make &amp;&amp; cp samtools ../ &amp;&amp; ls -als &amp;&amp; cd .. &amp;&amp; ls -als</action>
 				<action type="move_file">
-					<source>bin/samtools</source>
+					<source>samtools</source>
 					<destination>$INSTALL_DIR/bin</destination>
 				</action>
 				<action type="set_environment">
@@ -21,7 +21,7 @@
 	<package name="VarScan" version="2.3.6">
 		<install version="1.0">
 			<actions>
-				<action type="shell_command">wget http://downloads.sourceforge.net/project/varscan/VarScan.v2.3.6.jar</action>
+				<action type="shell_command">wget http://downloads.sourceforge.net/project/varscan/VarScan.v2.3.6.jar &amp;&amp; pwd &amp;&amp; ls -als</action>
 				<action type="move_file">
 					<source>VarScan.v2.3.6.jar</source>
 					<destination>$INSTALL_DIR/bin</destination>