Mercurial > repos > stef > qdnaseq

changeset 14:7be26321018b draft

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Uploaded
author stef
date Mon, 16 Jun 2014 11:21:23 -0400
parents 0a242c6cfdde
children 4472cc10b065
files tool_dependencies.xml
diffstat 1 files changed, 8 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- 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>