Mercurial > repos > fubar > differential_count_models

diff tool_dependencies.xml @ 71:f33aac17f15d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author fubar
date Tue, 18 Feb 2014 01:12:00 -0500
parents e4291e5a03c1
children a83f8effff05
line wrap: on
line diff
--- a/tool_dependencies.xml	Tue Feb 18 01:07:24 2014 -0500
+++ b/tool_dependencies.xml	Tue Feb 18 01:12:00 2014 -0500
@@ -24,8 +24,8 @@
                 <action type="shell_command">echo "biocLite(installme)" &gt;&gt; $INSTALL_DIR/runme.R</action>
                 <action type="shell_command">echo "install.packages(c('stringr','gplots'),dependencies=T,repos='http://cran.us.r-project.org')" &gt;&gt; $INSTALL_DIR/runme.R</action>
                 <action type="shell_command">echo "quit(save='no')" &gt;&gt; $INSTALL_DIR/runme.R</action>                
-                <action type="shell_command" />                
-                <action type="shell_command"> export PATH=$PATH &amp;&amp; echo "PATH=$PATH" &amp;&amp; export R_HOME=$R_HOME &amp;&amp; export R_LIBS=$R_LIBS &amp;&amp; R CMD BATCH $INSTALL_DIR/runme.R </action>
+                <action type="shell_command"> echo "PATH=$PATH"</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>
         </install>
         <readme>Installs some basic bioc packages for the edgeR wrapper and dependencies graphicsmagick (replaces imagemagick) and ghostscript for compressing R's bloated pdfs