--- a/README	Mon Mar 04 23:59:59 2013 -0500
+++ b/README	Tue Mar 05 00:01:44 2013 -0500
@@ -1,42 +1,9 @@
-This package is an installer for BLAST+ from NCBI
-
-Requirements:
-This package depends on the galaxy_protk package
-Please see instructions for the galaxy_protk package before installing
-
--------- ABOUT --------------
+This package is an installer for the MSGF+ search tool.
 
-BLAST Command Line Applications
-
-The NCBI Basic Local Alignment Search Tool (BLAST) finds regions of
-local similarity between sequences. The program compares nucleotide or
-protein sequences to sequence databases and calculates the statistical
-significance of matches. BLAST can be used to infer functional and
-evolutionary relationships between sequences as well as help identify
-members of gene families.
-
-For more information, visit http://blast.ncbi.nlm.nih.gov
+System Requirements. Ensure that you have the following packages installed on your system
+- unzip
+- java runtime 6 or higher
 
 
--------- LICENCE ------------
-
-
-                            PUBLIC DOMAIN NOTICE
-               National Center for Biotechnology Information
-
-  This software/database is a "United States Government Work" under the
-  terms of the United States Copyright Act.  It was written as part of
-  the author's official duties as a United States Government employee and
-  thus cannot be copyrighted.  This software/database is freely available
-  to the public for use. The National Library of Medicine and the U.S.
-  Government have not placed any restriction on its use or reproduction.
-
-  Although all reasonable efforts have been taken to ensure the accuracy
-  and reliability of the software and data, the NLM and the U.S.
-  Government do not and cannot warrant the performance or results that
-  may be obtained by using this software or data. The NLM and the U.S.
-  Government disclaim all warranties, express or implied, including
-  warranties of performance, merchantability or fitness for any particular
-  purpose.
-
-  Please cite the author in any work or product based on this material.
+Further information about MSGF+ can be found at
+http://proteomics.ucsd.edu/Software/MSGFPlus.html#documentation

--- a/repository_dependencies.xml	Mon Mar 04 23:59:59 2013 -0500
+++ b/repository_dependencies.xml	Tue Mar 05 00:01:44 2013 -0500
@@ -1,4 +1,10 @@
 <?xml version="1.0"?>
- <repositories description="Requires the protk rubygem to perform the install">
+<!-- <repositories description="protk-msgfplus requires the protk rubygem to install MSGF+">
+     <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 MSGF+">
      <repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="dac478a72c1d"/>
 </repositories>
\ No newline at end of file

--- a/tool_dependencies.xml	Mon Mar 04 23:59:59 2013 -0500
+++ b/tool_dependencies.xml	Tue Mar 05 00:01:44 2013 -0500
@@ -1,22 +1,22 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="blast" version="2.2.27">
+    <package name="msgfplus" version="20130227">
         <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_blast.sh $INSTALL_DIR 1.2.0</action>
+                <action type="shell_command">sh install_msgfplus.sh $INSTALL_DIR 1.2.0</action>
                 <action type="move_file">
-                    <source>install_blast.sh</source>
+                    <source>install_msgfplus.sh</source>
                     <destination>$INSTALL_DIR</destination>
                 </action>
                 <action type="set_environment">
-                    <environment_variable name="PROTK_BLAST_ROOT" action="set_to">$INSTALL_DIR</environment_variable>
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable name="PROTK_MSGFPLUS_ROOT" action="set_to">$INSTALL_DIR</environment_variable>
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
                 </action>
             </actions>
         </install>
         <readme>
-            Installs BLAST via the protk installer
+            Installs MSGF+ via the protk installer
         </readme>
     </package>