# HG changeset patch
# User iracooke
# Date 1362388943 18000
# Node ID 21cede3cfb9bd69964368d492d075c125c09685d
# Parent  5e1594a159564da20c6a80feb397ece2095832a1
Uploaded

diff -r 5e1594a15956 -r 21cede3cfb9b .DS_Store
Binary file .DS_Store has changed
diff -r 5e1594a15956 -r 21cede3cfb9b ._.DS_Store
Binary file ._.DS_Store has changed
diff -r 5e1594a15956 -r 21cede3cfb9b omssa.xml
--- a/omssa.xml	Sun Jan 06 20:03:20 2013 -0500
+++ b/omssa.xml	Mon Mar 04 04:22:23 2013 -0500
@@ -1,13 +1,17 @@
 <tool id="proteomics_search_omssa_1" name="OMSSA MSMS Search" version="1.0.0">
-	<requirements>
-		<requirement type="package">protkgem</requirement>
-	</requirements>
-	
+
+   <requirements>
+	    <requirement type="package" version="1.1.9">galaxy_protk</requirement>
+    	<requirement type="package" version="2.1.8">omssa</requirement>
+    	<requirement type="package" version="2.2.27">blast</requirement>
+   </requirements>
+
+
 	<description>Run an OMSSA MS/MS Search</description>
 		
 	<command>#if $database.source_select=="built_in":
-		omssa_search.rb -d $database.dbkey 
-		#else #omssa_search.rb -d $database.fasta_file
+		rvm 1.9.3@protk-1.1.9 do omssa_search.rb -d $database.dbkey 
+		#else #rvm 1.9.3@protk-1.1.9 do omssa_search.rb -d $database.fasta_file
 		#end if
 		
 		--var-mods='
diff -r 5e1594a15956 -r 21cede3cfb9b repository_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml	Mon Mar 04 04:22:23 2013 -0500
@@ -0,0 +1,10 @@
+<?xml version="1.0"?>
+<!-- <repositories description="Requires Proteomics Datatypes">
+     <repository toolshed="http://10.211.55.28:9009" name="proteomics_datatypes" owner="iracooke" changeset_revision="699a890a9d99"/>
+ </repositories>
+ -->
+
+ 
+  <repositories description="Requires the protk rubygem to install omssa">
+     <repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="51f7c347c955"/>
+</repositories>
\ No newline at end of file
diff -r 5e1594a15956 -r 21cede3cfb9b tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Mar 04 04:22:23 2013 -0500
@@ -0,0 +1,29 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <!-- <package name="galaxy_protk" version="1.1.9">
+	     <repository toolshed="http://10.211.55.28:9009" name="galaxy_protk" owner="iracooke" changeset_revision="5610168f3b53"/>
+    </package>
+
+    <package name="blast" version="2.2.27">
+        <repository toolshed="http://10.211.55.28:9009" name="protk_blast" owner="iracooke" changeset_revision="0f3b7bbdfdd4" />
+    </package>
+
+    <package name="omssa" version="2.1.8">
+        <repository toolshed="http://10.211.55.28:9009" name="protk_omssa" owner="iracooke" changeset_revision="117faa58df2a" />
+    </package> -->
+
+<package name="galaxy_protk" version="1.1.9">
+	     <repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="51f7c347c955"/>
+    </package>
+
+    <package name="blast" version="2.2.27">
+        <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_blast" owner="iracooke" changeset_revision="88ada6a29993" />
+    </package>
+
+    <package name="omssa" version="2.1.8">
+        <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_omssa" owner="iracooke" changeset_revision="e924c0d646d0" />
+    </package>
+
+
+
+</tool_dependency>
\ No newline at end of file