Repository 'edger_test'
hg clone https://testtoolshed.g2.bx.psu.edu/repos/fubar/edger_test

Changeset 41:4afd763390e6 (2013-06-13)
Previous changeset 40:5c211b875782 (2013-06-13) Next changeset 42:697272b8ef42 (2013-06-15)
Commit message:
Uploaded
modified:
rgedgeR/tool_dependencies.xml
removed:
rgedgeR/installBioC.R
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diff -r 5c211b875782 -r 4afd763390e6 rgedgeR/installBioC.R
--- a/rgedgeR/installBioC.R Thu Jun 13 01:41:21 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
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@@ -1,4 +0,0 @@
-source('http://bioconductor.org/biocLite.R')
-installme=c('edgeR','limma','DESeq','DEXSeq','ggplot2','gplots')
-biocLite()
-biocLite(installme)
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diff -r 5c211b875782 -r 4afd763390e6 rgedgeR/tool_dependencies.xml
--- a/rgedgeR/tool_dependencies.xml Thu Jun 13 01:41:21 2013 -0400
+++ b/rgedgeR/tool_dependencies.xml Thu Jun 13 01:51:54 2013 -0400
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@@ -16,12 +16,12 @@
                 <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">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>
-        <readme>Installs some basic bioc packages for the edgeR tool
+        <readme>Installs some basic bioc packages for the edgeR wrapper
+        It's clunky but this is the only way I could get anything installed into the package_r3 R
        </readme>
     </package>
 </tool_dependency>