Mercurial > repos > fubar > differential_count_models

diff tool_dependencies.xml @ 93:34ef458b7fd9 draft

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Uploaded
author fubar
date Sun, 02 Mar 2014 22:25:13 -0500
parents 6fb919a3bff4
children 9414bbf5579b
line wrap: on
line diff
--- a/tool_dependencies.xml	Sun Mar 02 22:21:47 2014 -0500
+++ b/tool_dependencies.xml	Sun Mar 02 22:25:13 2014 -0500
@@ -17,17 +17,8 @@
                         <package name="r303" version="3.0.3" />
                     </repository>
                 </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 $INSTALL_DIR/runme.R </action>
+                <action type="make_directory">$INSTALL_DIR</action>               
+                <action type="shell_command">export PATH=$PATH &amp;&amp; R CMD BATCH 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