# HG changeset patch
# User iracooke
# Date 1393998988 18000
# Node ID 244a1163f1320770ad5bf382d272957b9b79455a
# Parent  9b21b161ac9705d8dd95ababcddbefef9fe5df31
Uploaded

diff -r 9b21b161ac97 -r 244a1163f132 tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Mar 03 00:20:38 2014 -0500
+++ b/tool_dependencies.xml	Wed Mar 05 00:56:28 2014 -0500
@@ -3,15 +3,22 @@
     <package name="msgfplus" version="20140210">
         <install version="1.0">
             <actions>
-                <action type="download_by_url">http://proteomics.ucsd.edu/Software/MSGFPlus/MSGFPlus.20140210.zip</action>
+                <action type="download_by_url">https://proteomics.ucsd.edu/Downloads/MSGFPlus.20140210.zip</action>
+                <action type="move_file">
+                    <source>MSGFPlus.jar</source>
+                    <destination>$INSTALL_DIR</destination>
+                </action>
                 <action type="set_environment">
+                    <environment_variable name="MSGFPLUS_ROOT" action="set_to">$INSTALL_DIR</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 MS-GF+. Requires java 1.6 or greater
+            Downloads and installs MSGF+.
+            https://proteomics.ucsd.edu/
+            Java 1.6 is required to run MSGF+.
         </readme>
     </package>
-
 </tool_dependency>