# HG changeset patch
# User iracooke@gmail.com
# Date 1380168553 -36000
# Node ID e79b95501048633fc35bf5ba680a10a2e80c77c5
# Parent  cd0d5e6b9a92446aff1cee47996f25d83ae051d3
Use setup_rvm action

diff -r cd0d5e6b9a92 -r e79b95501048 omssa.xml
--- a/omssa.xml	Thu Jun 06 15:37:22 2013 +1000
+++ b/omssa.xml	Thu Sep 26 14:09:13 2013 +1000
@@ -9,7 +9,7 @@
 
 	<description>Run an OMSSA MS/MS Search</description>
 		
-	<command>rvm 1.9.3@protk-1.2.2 do omssa_search.rb
+	<command>omssa_search.rb
 
 		#if $database.source_select=="built_in":
 		-d $database.dbkey 
diff -r cd0d5e6b9a92 -r e79b95501048 repository_dependencies.xml
--- a/repository_dependencies.xml	Thu Jun 06 15:37:22 2013 +1000
+++ b/repository_dependencies.xml	Thu Sep 26 14:09:13 2013 +1000
@@ -3,10 +3,10 @@
 
 	<repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="proteomics_datatypes" owner="iracooke" changeset_revision="7101f7e4b00b"/>
 
-    <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="32c643142290" prior_installation_required="True"/>
+<!--     <repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="dac478a72c1d" prior_installation_required="True"/>
 
-    <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="protk_blast" owner="iracooke" changeset_revision="a1b21b3844c8"/>
+    <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_blast" owner="iracooke" changeset_revision="0d86d29aaed6" />
 
-    <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="protk_omssa" owner="iracooke" changeset_revision="b386c6c95d0e"/>
-
+    <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_omssa" owner="iracooke" changeset_revision="f77532db59b6" />
+ -->
 </repositories>
diff -r cd0d5e6b9a92 -r e79b95501048 tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Jun 06 15:37:22 2013 +1000
+++ b/tool_dependencies.xml	Thu Sep 26 14:09:13 2013 +1000
@@ -1,18 +1,18 @@
 <?xml version="1.0"?>
 <tool_dependency>
-
-    <package name="galaxy_protk" version="1.2.2">
-         <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="32c643142290" prior_installation_required="True"/>
-    </package>
-
-    <package name="blast" version="2.2.27">
-        <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="protk_blast" owner="iracooke" changeset_revision="a1b21b3844c8"/>
-    </package>
-
-    <package name="omssa" version="2.1.9">
-        <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="protk_omssa" owner="iracooke" changeset_revision="b386c6c95d0e"/>
-    </package>
-
-
+	<package name="protk_omssa" version="2.1.9">
+		<install version="1.0">
+    	<actions>
+     		<action type="setup_rvm" ruby="1.9.3-p448">
+     		<gem version="1.2.4">protk</gem>
+     		</action>
+ 			<action type="shell_command">protk_setup.rb blast</action>
+ 			<action type="shell_command">protk_setup.rb omssa</action>
+		</actions>
+    		</install>
+   		<readme>
+               RVM Example
+             </readme>
+        </package>
 
 </tool_dependency>