Mercurial > repos > fubar > differential_count_models

diff tool_dependencies.xml @ 69:919822102c86 draft

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author fubar
date Mon, 17 Feb 2014 18:46:46 -0500
parents a2016dfb1de5
children e4291e5a03c1
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--- a/tool_dependencies.xml	Mon Feb 17 18:42:08 2014 -0500
+++ b/tool_dependencies.xml	Mon Feb 17 18:46:46 2014 -0500
@@ -24,7 +24,7 @@
                 <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; $INSTALL_DIR/runme.R</action>                
-                <action type="shell_command"> export PATH=$PATH &amp;&amp; export R_HOME=$R_HOME &amp;&amp; export R_LIBS=$R_LIBS &amp;&amp; R CMD BATCH $INSTALL_DIR/runme.R </action>
+                <action type="shell_command"> export PATH=$PATH &amp;&amp; export R_HOME=$R_HOME &amp;&amp; export R_LIBS=$R_LIBS &amp;&amp; $R_PATH/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