Mercurial > repos > fubar > edger_test

changeset 39:d110c5bb0ad3 draft

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Uploaded
author fubar
date Thu, 13 Jun 2013 01:36:22 -0400
parents ba361e7ebc17
children 5c211b875782
files rgedgeR/tool_dependencies.xml
diffstat 1 files changed, 6 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/rgedgeR/tool_dependencies.xml	Thu Jun 13 01:09:25 2013 -0400
+++ b/rgedgeR/tool_dependencies.xml	Thu Jun 13 01:36:22 2013 -0400
@@ -11,7 +11,12 @@
                         <package name="r3" version="3.0.1" />
                     </repository>
                 </action>
-                <action type="shell_command">R CMD BATCH rgedgeR/installBioC.R </action>
+                <action type="make_directory">$INSTALL_DIR</action>
+                <action type="shell_command">echo source('http://bioconductor.org/biocLite.R') &gt; $INSTALL_DIR/runme.R</action>
+                <action type="shell_command">echo installme=c('edgeR','limma','DESeq','DEXSeq','ggplot2','gplots') &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; $INSTALL_DIR/runme.R</action>
+                <action type="shell_command"> export PATH=$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 tool