# HG changeset patch
# User stef
# Date 1402994009 14400
# Node ID 160190da7976f3854d13bf39985ad7a36e507113
# Parent  16a21a760ba255cd2e7d9d80f056260b2dbecaf6
Uploaded

diff -r 16a21a760ba2 -r 160190da7976 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Jun 17 04:23:28 2014 -0400
+++ b/tool_dependencies.xml	Tue Jun 17 04:33:29 2014 -0400
@@ -1,10 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
 	
-	<actions>                                
-		<action type="move_file"><source>QDNAseq.R</source><destination>$REPOSITORY_INSTALL_DIR</destination></action>
-	</actions>
-	
 	<set_environment version="1.0">
      	<environment_variable name="QDNASEQ_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
      </set_environment>
@@ -16,7 +12,15 @@
 	<package name="bioc_qdnaseq" version="1.0.5">
 		<install version="1.0">
 			<actions>
-				<action type="shell_command">echo "[DEBUG] WORKING DIR:" &amp;&amp; pwd</action>
+				
+				<action type="shell_command">echo "[DEBUG] BEFORE:" &amp;&amp; pwd</action>
+				<action type="shell_command">echo "[DEBUG] DIR LISTING:" &amp;&amp; ls -l</action>
+				<action type="move_file">
+					<source>QDNAseq.R</source>
+					<destination>$INSTALL_DIR</destination>
+				</action>
+				
+				<action type="shell_command">echo "[DEBUG] AFTER:" &amp;&amp; pwd</action>
 				<action type="shell_command">echo "[DEBUG] DIR LISTING:" &amp;&amp; ls -l</action>
 
 				<action type="set_environment_for_install">