Mercurial > repos > big-tiandm > degseq

diff tool_dependencies.xml @ 14:e10ada1be34d draft

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Uploaded
author big-tiandm
date Fri, 14 Nov 2014 23:01:13 -0500
parents 96961ac4f745
children 1f49db503877
line wrap: on
line diff
--- a/tool_dependencies.xml	Fri Nov 14 21:24:56 2014 -0500
+++ b/tool_dependencies.xml	Fri Nov 14 23:01:13 2014 -0500
@@ -5,18 +5,25 @@
     </set_environment>
 
 	<package name="R" version="3.0.1">
-	   <repository changeset_revision="c5ff6dd33c79" name="package_r_3_0_1" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
+	   <repository changeset_revision="c5ff6dd33c79" name="package_r_3_0_1" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" prior_installation_required="True"/>
 	</package>
 
 	<package name="degseq" version="1.20.0">
 		<install version="1.0">
 		   <actions>
 		      <action type="set_environment_for_install">
-                    <repository changeset_revision="c5ff6dd33c79" name="package_r_3_0_1" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
+                    <repository changeset_revision="c5ff6dd33c79" name="package_r_3_0_1" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" prior_installation_required="True">
                         <package name="R" version="3.0.1" />
                     </repository>
               </action>
 		      <action type="shell_command">R CMD BATCH $REPOSITORY_INSTALL_DIR/install_DEG.R </action>
+
+			  <action type="shell_command">RPATH=`which R` </action>
+
+			  <action type="set_environment">
+                 <environment_variable name="PATH" action="prepend_to">$RPATH</environment_variable>
+              </action>
+		   
 		   </actions>
 		</install>