# HG changeset patch
# User pieter.lukasse@wur.nl
# Date 1391784938 -3600
# Node ID 1a6fa343b981164ba42bbf8c1b562130b0e47582
# Parent  f47b24cccf88da22d84fb50a3592e1b77733ea57
Adding auto install for proteowizard dependency

diff -r f47b24cccf88 -r 1a6fa343b981 MassComb.jar
Binary file MassComb.jar has changed
diff -r f47b24cccf88 -r 1a6fa343b981 masscomb_dbsearch_converter.xml
--- a/masscomb_dbsearch_converter.xml	Fri Feb 07 15:09:53 2014 +0100
+++ b/masscomb_dbsearch_converter.xml	Fri Feb 07 15:55:38 2014 +0100
@@ -1,5 +1,9 @@
-<tool name="DB search converter" id="masscomb_dbsearch_converter" version="1.0.1">
+<tool name="DB search converter" id="masscomb_dbsearch_converter" version="1.0.5">
 	<description> Convert search results to MzIdentML (aka mzid) format</description>
+	<requirements>
+		<requirement type="set_environment">PWIZ_3_0_5622_PATH</requirement>
+		<requirement type="package" version="3.05622">proteowizard</requirement>
+	</requirements>
 	<!-- 
 	   For remote debugging start you listener on port 8000 and use the following as command interpreter:
 	       java -jar -Xdebug -Xrunjdwp:transport=dt_socket,address=D0100564.wurnet.nl:8000 
diff -r f47b24cccf88 -r 1a6fa343b981 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Feb 07 15:09:53 2014 +0100
+++ b/tool_dependencies.xml	Fri Feb 07 15:55:38 2014 +0100
@@ -22,7 +22,24 @@
 Ensures XTandem is installed. 
         </readme>
     </package>
+    <package name="proteowizard" version="3.05622">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://toolshed.g2.bx.psu.edu/repos/pieterlukasse/prims_masscomb/raw-file/tip/pwiz-bin-linux-x86_64-gcc48-release-3_0_5622.tar.bz2</action>
+                <action type="move_directory_files">
+					<source_directory>.</source_directory>
+					<destination_directory>$INSTALL_DIR/pwiz_3_0_5622</destination_directory>
+				</action>
+				<action type="set_environment">
+                    <environment_variable name="PWIZ_3_0_5622_PATH" action="set_to">$INSTALL_DIR/pwiz_3_0_5622</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+Ensures ProteoWizard binaries are installed. 
+        </readme>
+    </package>
 	<set_environment version="1.0">
-        <environment_variable name="XTANDEM_12_10_01_PATH" action="set_to">$INSTALL_DIR/tandem-linux-12-10-01-1</environment_variable>   
+        <environment_variable name="PWIZ_3_0_5622_PATH" action="set_to">$INSTALL_DIR/pwiz_3_0_5622</environment_variable>   
     </set_environment>
 </tool_dependency>
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