Mercurial > repos > fubar > edger_test

changeset 40:5c211b875782 draft

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Uploaded
author fubar
date Thu, 13 Jun 2013 01:41:21 -0400
parents d110c5bb0ad3
children 4afd763390e6
files rgedgeR/tool_dependencies.xml
diffstat 1 files changed, 6 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/rgedgeR/tool_dependencies.xml	Thu Jun 13 01:36:22 2013 -0400
+++ b/rgedgeR/tool_dependencies.xml	Thu Jun 13 01:41:21 2013 -0400
@@ -12,10 +12,12 @@
                     </repository>
                 </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">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">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>
             </actions>
         </install>