Mercurial > repos > fubar > differential_count_models

diff tool_dependencies.xml @ 70:e4291e5a03c1 draft

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Uploaded
author fubar
date Tue, 18 Feb 2014 01:07:24 -0500
parents 919822102c86
children f33aac17f15d
line wrap: on
line diff
--- a/tool_dependencies.xml	Mon Feb 17 18:46:46 2014 -0500
+++ b/tool_dependencies.xml	Tue Feb 18 01:07:24 2014 -0500
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="r302" version="3.0.2">
-        <repository changeset_revision="ce4a3c48dbd7" name="package_r302" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
+        <repository changeset_revision="c161b72d384e" name="package_r302" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
     </package>
     <package name="ghostscript" version="9.10">
         <repository changeset_revision="9345d2740f0c" name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
@@ -13,7 +13,7 @@
         <install version="1.0"> 
             <actions>
                 <action type="set_environment_for_install">
-                    <repository changeset_revision="ce4a3c48dbd7" name="package_r302" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/">
+                    <repository changeset_revision="c161b72d384e" name="package_r302" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/">
                         <package name="r302" version="3.0.2" />
                     </repository>
                 </action>
@@ -24,7 +24,8 @@
                 <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; $INSTALL_DIR/runme.R</action>                
-                <action type="shell_command"> export PATH=$PATH &amp;&amp; export R_HOME=$R_HOME &amp;&amp; export R_LIBS=$R_LIBS &amp;&amp; $R_PATH/R CMD BATCH $INSTALL_DIR/runme.R </action>
+                <action type="shell_command" />                
+                <action type="shell_command"> export PATH=$PATH &amp;&amp; echo "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 wrapper and dependencies graphicsmagick (replaces imagemagick) and ghostscript for compressing R's bloated pdfs