Mercurial > repos > fubar > edger_test

diff rgedgeR/tool_dependencies.xml @ 49:c4f8c9a00c0e draft

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Uploaded
author fubar
date Fri, 26 Jul 2013 22:47:38 -0400
parents e622f665c61c
children
line wrap: on
line diff
--- a/rgedgeR/tool_dependencies.xml	Fri Jul 26 22:04:58 2013 -0400
+++ b/rgedgeR/tool_dependencies.xml	Fri Jul 26 22:47:38 2013 -0400
@@ -1,21 +1,22 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="package_r3" version="3.0.1">
-        <repository changeset_revision="6f249fadd4ec" name="package_r3" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
+    <package name="r3" version="3.0.1">
+        <repository changeset_revision="1ffaf8412079" name="package_r3" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
     </package>
     <package name="biocbasics" version="2.12">
         <install version="1.0"> 
             <actions>
                 <action type="set_environment_for_install">
-                    <repository changeset_revision="6f249fadd4ec" name="package_r3" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/">
+                    <repository changeset_revision="1ffaf8412079" name="package_r3" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/">
                         <package name="r3" version="3.0.1" />
                     </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','DESeq2','gplots')" &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)" &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>