Mercurial > repos > fubar > edger_test

changeset 43:1212dc390f4f draft

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Uploaded
author fubar
date Mon, 17 Jun 2013 04:40:18 -0400
parents 697272b8ef42
children 590068a0c820
files rgedgeR/tool_dependencies.xml
diffstat 1 files changed, 4 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/rgedgeR/tool_dependencies.xml	Sat Jun 15 03:49:46 2013 -0400
+++ b/rgedgeR/tool_dependencies.xml	Mon Jun 17 04:40:18 2013 -0400
@@ -17,8 +17,10 @@
                 <action type="shell_command">echo "biocLite()" &gt;&gt; $INSTALL_DIR/runme.R</action>
                 <action type="shell_command">echo "biocLite(installme)" &gt;&gt; $INSTALL_DIR/runme.R</action>
                 <action type="shell_command">echo "quit(save='no')" &gt;&gt; $INSTALL_DIR/runme.R</action>                
-                <action type="shell_command"> export PATH=$PATH &amp;&amp; export R_HOME=$R_HOME &amp;&amp; export R_LIBS=$R_LIBS &amp;&amp; R CMD BATCH $INSTALL_DIR/runme.R  </action>
-            </actions>
+                <action type="shell_command"> export PATH=$PATH &amp;&amp; export R_HOME=$R_HOME &amp;&amp; export R_LIBS=$R_LIBS &amp;&amp;
+                 R CMD BATCH $INSTALL_DIR/runme.R &gt; $INSTALL_DIR/install.log </action>
+                <action type="shell_command">cat $INSTALL_DIR/install.log</action>
+             </actions>
         </install>
         <readme>Installs some basic bioc packages for the edgeR wrapper
         It's clunky but this is the only way I could get anything installed into the package_r3 R