changeset 41:4afd763390e6 draft

Uploaded
author fubar
date Thu, 13 Jun 2013 01:51:54 -0400
parents 5c211b875782
children 697272b8ef42
files rgedgeR/installBioC.R rgedgeR/tool_dependencies.xml
diffstat 2 files changed, 3 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/rgedgeR/installBioC.R	Thu Jun 13 01:41:21 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-source('http://bioconductor.org/biocLite.R')
-installme=c('edgeR','limma','DESeq','DEXSeq','ggplot2','gplots')
-biocLite()
-biocLite(installme)
--- 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
@@ -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>