# HG changeset patch
# User stef
# Date 1402994588 14400
# Node ID eefb834376ba84629c65b44c29a9edbb0347383b
# Parent  03251c8d6b469ecb57d1e44b3b53c8dd70f5ea65
Uploaded

diff -r 03251c8d6b46 -r eefb834376ba tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Jun 17 04:36:18 2014 -0400
+++ b/tool_dependencies.xml	Tue Jun 17 04:43:08 2014 -0400
@@ -12,11 +12,13 @@
 	<package name="bioc_qdnaseq" version="1.0.5">
 		<install version="1.0">
 			<actions>
+				<action type="shell_command">echo "[DEBUG] INSTALL DIR: $INSTALL_DIR"</action>
+				<action type="shell_command">echo "[DEBUG] REPOS INSTALL DIR: $REPOSITORY_INSTALL_DIR"</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>$INSTALL_DIR/QDNAseq.R</source>
+					<source>$REPOSITORY_INSTALL_DIR/QDNAseq.R</source>
 					<destination>./</destination>
 				</action>
 				
@@ -32,7 +34,8 @@
 						<environment_variable action="prepend_to" name="R_LIBS">$INSTALL_DIR/bin</environment_variable>
 				</action>
 				<action type="shell_command">echo "[DEBUG] NOW ABOUT TO DOWNLOAD"</action>
-				<action type="shell_command">wget http://bioconductor.org/packages/release/bioc/src/contrib/QDNAseq_1.0.5.tar.gz</action>
+				
+				<action type="download_file">http://bioconductor.org/packages/release/bioc/src/contrib/QDNAseq_1.0.5.tar.gz</action>
 				
 				<action type="shell_command">echo "[DEBUG] WORKING DIR:" &amp;&amp; pwd</action>
 				<action type="shell_command">echo "[DEBUG] DIR LISTING:" &amp;&amp; ls -l</action>