# HG changeset patch
# User fubar
# Date 1393820448 18000
# Node ID 851f3946c9d93ece17595174e9281ad295700906
# Parent  df7ce9396d86b726f73f7eb6301e7a2cd56c0a5c
Uploaded

diff -r df7ce9396d86 -r 851f3946c9d9 tool_dependencies.xml
--- a/tool_dependencies.xml	Sun Mar 02 23:10:55 2014 -0500
+++ b/tool_dependencies.xml	Sun Mar 02 23:20:48 2014 -0500
@@ -17,12 +17,17 @@
                         <package name="r303" version="3.0.3" />
                     </repository>
                 </action>
-                <action type="make_directory">$INSTALL_DIR</action>  
-                <action type="move_file">
-                    <source>runme.R</source>
-                    <destination>$INSTALL_DIR</destination>
-                </action>
-                <action type="shell_command">export PATH=$PATH &amp;&amp; R CMD BATCH $INSTALL_DIR/runme.R </action>
+                <action type="make_directory">$INSTALL_DIR</action>
+                <action type="shell_command">echo 'bioclite = "http://bioconductor.org/biocLite.R"' &gt; $INSTALL_DIR/runme.R</action>
+                <action type="shell_command">echo "source(bioclite)" &gt;&gt; $INSTALL_DIR/runme.R</action>
+                <action type="shell_command">echo 'installme=c("edgeR","limma","DESeq","DESeq2")' &gt;&gt; $INSTALL_DIR/runme.R</action>
+                <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 '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; $INSTALL_DIR/runme.R</action>                
+                <action type="shell_command">echo "PATH=$PATH 1&gt;&amp;2"</action>                
+                <action type="shell_command">echo "R_PATH=$R_PATH 1&gt;&amp;2"</action>                
+                <action type="shell_command">export PATH=$PATH &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