diff tool_dependencies.xml @ 91:6fb919a3bff4 draft

Uploaded

--- a/tool_dependencies.xml	Thu Feb 27 05:29:51 2014 -0500
+++ b/tool_dependencies.xml	Sun Mar 02 19:49:16 2014 -0500
@@ -1,31 +1,33 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="r303" version="3.0.3">
-        <repository changeset_revision="826f08ed8859" name="package_r303" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
-    </package>
     <package name="ghostscript" version="9.07">
         <repository changeset_revision="10222a7db54c" name="package_ghostscript_9_07" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
     </package>
     <package name="graphicsmagick" version="1.3.18">
         <repository changeset_revision="2fd4eb971ba5" name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
     </package>
+    <package name="r303" version="3.0.3">
+        <repository changeset_revision="4c934f6b342e" name="package_r303" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
+    </package>
     <package name="biocbasics" version="2.14">
         <install version="1.0"> 
             <actions>
                 <action type="set_environment_for_install">
-                    <repository changeset_revision="826f08ed8859" name="package_r303" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/">
+                    <repository changeset_revision="4c934f6b342e" name="package_r303" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/">
                         <package name="r303" version="3.0.3" />
                     </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 "bioclite = 'http://bioconductor.org/biocLite.R'" &gt; $INSTALL_DIR/runme.R</action>
+                <action type="shell_command">echo "source(bioclite)" &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,repos='http://cran.us.r-project.org')" &gt;&gt; $INSTALL_DIR/runme.R</action>
                 <action type="shell_command">echo "quit(save='no')" &gt;&gt; $INSTALL_DIR/runme.R</action>                
                 <action type="shell_command">echo "PATH=$PATH 1&gt;&amp;2"</action>                
-                <action type="shell_command">export PATH=$PATH &amp;&amp; R CMD BATCH $INSTALL_DIR/runme.R </action>
+                <action type="shell_command">echo "R_PATH=$R_PATH 1&gt;&amp;2"</action>                
+                <action type="shell_command">export PATH=$PATH &amp;&amp; $R_PATH/R CMD BATCH $INSTALL_DIR/runme.R </action>
             </actions>
         </install>
         <readme>Installs some basic bioc packages for the edgeR wrapper and dependencies graphicsmagick (replaces imagemagick) and ghostscript for compressing R's bloated pdfs