# HG changeset patch
# User stef
# Date 1402932083 14400
# Node ID 7be26321018bcd803a79254c02ba06628d3b092f
# Parent  0a242c6cfdde57eb9dcbf9403bc28ba0a4cfbecf
Uploaded

diff -r 0a242c6cfdde -r 7be26321018b tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Jun 16 08:23:31 2014 -0400
+++ b/tool_dependencies.xml	Mon Jun 16 11:21:23 2014 -0400
@@ -12,6 +12,8 @@
 	<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] DIR LISTING:" &amp;&amp; ls -l</action>
 				<!--<action type="download_by_url">
 					http://bioconductor.org/packages/release/bioc/src/contrib/QDNAseq_1.0.5.tar.gz
 				</action>-->
@@ -23,8 +25,13 @@
 				<action type="set_environment">
 						<environment_variable action="prepend_to" name="R_LIBS">$INSTALL_DIR/bin</environment_variable>
 				</action>
+				<action type="shell_command">echo "[DEBUG] NOW ABOUT TO DOWNLOAD</action>
 				<action type="shell_command">wget http://bioconductor.org/packages/release/bioc/src/contrib/QDNAseq_1.0.5.tar.gz</action>
-				<action type="shell_command">ls -l &amp;&amp; echo "print dir" &amp;&amp; pwd</action>
+				
+				<action type="shell_command">echo "[DEBUG] WORKING DIR:" &amp;&amp; pwd</action>
+				<action type="shell_command">echo "[DEBUG] DIR LISTING:" &amp;&amp; ls -l</action>
+				
+				<action type="shell_command">echo "[DEBUG] NOW ABOUT TO INSTALL"</action>
 				<action type="shell_command">export R_LIBS=$INSTALL_DIR &amp;&amp; R CMD INSTALL --build QDNAseq_1.0.5.tar.gz</action>
 				<!--<action type="shell_command">R CMD INSTALL QDNAseq_1.0.5.tar.gz</action>-->
 			</actions>