# HG changeset patch
# User Ira Cooke <iracooke@gmail.com>
# Date 1370783812 18000
# Node ID 8f3813e7b0a668f07a1288eec9436ed312a36922
# Parent  f77532db59b6ccf3a8318e9515604ba3d61ec769
Update

diff -r f77532db59b6 -r 8f3813e7b0a6 repository_dependencies.xml
--- a/repository_dependencies.xml	Tue Mar 05 00:04:49 2013 -0500
+++ b/repository_dependencies.xml	Sun Jun 09 08:16:52 2013 -0500
@@ -3,7 +3,6 @@
      <repository toolshed="http://10.211.55.28:9009" name="galaxy_protk" owner="iracooke" changeset_revision="2562efef05cb"/>
 </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="dac478a72c1d"/>
-</repositories>
\ No newline at end of file
+<repositories description="Requires the protk rubygem to install omssa">
+     <repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="c25df71f7b68"/>
+</repositories>
diff -r f77532db59b6 -r 8f3813e7b0a6 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Mar 05 00:04:49 2013 -0500
+++ b/tool_dependencies.xml	Sun Jun 09 08:16:52 2013 -0500
@@ -1,10 +1,13 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="omssa" version="2.1.8">
+    <package name="galaxy_protk" version="1.2.2">
+         <repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="c25df71f7b68" prior_installation_required="True"/>
+    </package>
+    <package name="omssa" version="2.1.9">
         <install version="1.0">
             <actions>
                 <action type="download_by_url">https://dl.dropbox.com/u/226794/galaxy_protk.tar.gz</action>
-                <action type="shell_command">sh install_omssa.sh $INSTALL_DIR 1.2.0</action>
+                <action type="shell_command">sh install_omssa.sh $INSTALL_DIR 1.2.2</action>
                 <action type="move_file">
                     <source>install_omssa.sh</source>
                     <destination>$INSTALL_DIR</destination>
@@ -17,7 +20,12 @@
         </install>
         <readme>
             Installs OMSSA via the protk installer
+            By default OMSSA will run with as many threads as are available. 
+            You can limit the number of threads by setting the environment 
+            variable PROTK_OMSSA_NTHREADS to the number of threads you would like OMSSA to use.
+            Please see http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies 
+            for details on setting environment variables for galaxy tools
         </readme>
     </package>
 
-</tool_dependency>
\ No newline at end of file
+</tool_dependency>