# HG changeset patch
# User Ira Cooke <iracooke@gmail.com>
# Date 1370497095 -36000
# Node ID cc7c5f92759eae43271731c262945c37be0bb098
# Parent  0df91f1ff47708f47b61f73a2f9709d844c43c32
Fix

diff -r 0df91f1ff477 -r cc7c5f92759e repository_dependencies.xml
--- a/repository_dependencies.xml	Mon Jun 03 16:28:18 2013 +1000
+++ b/repository_dependencies.xml	Thu Jun 06 15:38:15 2013 +1000
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
 <repositories description="Proteomics datatypes and the TPP">
      <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="protk_trans_proteomic_pipeline" owner="iracooke" changeset_revision="fe02e5e93877"/>
+     <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="protk_trans_proteomic_pipeline" owner="iracooke" changeset_revision="5894fb541275"/>
  </repositories>
diff -r 0df91f1ff477 -r cc7c5f92759e tandem.xml
--- a/tandem.xml	Mon Jun 03 16:28:18 2013 +1000
+++ b/tandem.xml	Thu Jun 06 15:38:15 2013 +1000
@@ -1,7 +1,7 @@
 <tool id="proteomics_search_tandem_1" name="X!Tandem MSMS Search" version="1.0.1">
 
    <requirements>
-    <requirement type="package" version="1.2.0">galaxy_protk</requirement>
+    <requirement type="package" version="1.2.2">galaxy_protk</requirement>
     <requirement type="package" version="4.6.1">trans_proteomic_pipeline</requirement>
    </requirements>
 
@@ -9,8 +9,8 @@
 
 	<command>
 		#if $database.source_select=="built_in":
-		rvm 1.9.3@protk-1.2.0 do tandem_search.rb -d $database.dbkey 
-		#else #rvm 1.9.3@protk-1.2.0 do tandem_search.rb -d $database.fasta_file
+		rvm 1.9.3@protk-1.2.2 do tandem_search.rb -d $database.dbkey 
+		#else #rvm 1.9.3@protk-1.2.2 do tandem_search.rb -d $database.fasta_file
 		#end if
 
 		--var-mods='
diff -r 0df91f1ff477 -r cc7c5f92759e tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Jun 03 16:28:18 2013 +1000
+++ b/tool_dependencies.xml	Thu Jun 06 15:38:15 2013 +1000
@@ -1,10 +1,10 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="galaxy_protk" version="1.2.0">
-	     <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="8bb76a3347c9" prior_installation_required="True"/>
+    <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="trans_proteomic_pipeline" version="4.6.1">
-        <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="protk_trans_proteomic_pipeline" owner="iracooke" changeset_revision="fe02e5e93877"/>
+        <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="protk_trans_proteomic_pipeline" owner="iracooke" changeset_revision="5894fb541275"/>
     </package>
 </tool_dependency>