From 5d8ded8f8e02ebe1a0dabea0eb98d53a4643a414 Mon Sep 17 00:00:00 2001
From: Lutz Fischer <lfischer@staffmail.ed.ac.uk>
Date: Tue, 31 Mar 2015 17:21:47 +0100
Subject: [PATCH] changed maven config to include all dependencies and enable
 creation of a jar-that includes all dependencies

---
 nb-configuration.xml | 18 +++++++++---------
 pom.xml              | 44 +++++++++++++++++++++++++++++++++++++++++++-
 2 files changed, 52 insertions(+), 10 deletions(-)

diff --git a/nb-configuration.xml b/nb-configuration.xml
index 1cdd454..0e565c6 100644
--- a/nb-configuration.xml
+++ b/nb-configuration.xml
@@ -1,19 +1,19 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project-shared-configuration>
+<?xml version="1.0" encoding="UTF-8"?>
+<project-shared-configuration>
     <!--
 This file contains additional configuration written by modules in the NetBeans IDE.
 The configuration is intended to be shared among all the users of project and
 therefore it is assumed to be part of version control checkout.
 Without this configuration present, some functionality in the IDE may be limited or fail altogether.
--->
-    <properties xmlns="http://www.netbeans.org/ns/maven-properties-data/1">
+-->
+    <properties xmlns="http://www.netbeans.org/ns/maven-properties-data/1">
         <!--
 Properties that influence various parts of the IDE, especially code formatting and the like. 
 You can copy and paste the single properties, into the pom.xml file and the IDE will pick them up.
 That way multiple projects can share the same settings (useful for formatting rules for example).
 Any value defined here will override the pom.xml file value but is only applicable to the current project.
--->
-        <netbeans.hint.license>apache20</netbeans.hint.license>
-        <org-netbeans-modules-javascript2-requirejs.enabled>false</org-netbeans-modules-javascript2-requirejs.enabled>
-    </properties>
-</project-shared-configuration>
+-->
+        <netbeans.hint.license>apache20</netbeans.hint.license>
+        <org-netbeans-modules-javascript2-requirejs.enabled>false</org-netbeans-modules-javascript2-requirejs.enabled>
+    </properties>
+</project-shared-configuration>
diff --git a/pom.xml b/pom.xml
index a9a2162..5c85561 100644
--- a/pom.xml
+++ b/pom.xml
@@ -11,10 +11,52 @@
             <artifactId>jmzidentml</artifactId>
             <version>1.1.3</version>
         </dependency>
+        <dependency>
+            <groupId>commons-io</groupId>
+            <artifactId>commons-io</artifactId>
+            <version>2.4</version>
+            <scope>runtime</scope>
+        </dependency>
+        <dependency>
+            <groupId>commons-logging</groupId>
+            <artifactId>commons-logging</artifactId>
+            <version>1.2</version>
+            <scope>runtime</scope>
+        </dependency>
+        <dependency>
+            <groupId>xxindex</groupId>
+            <artifactId>xxindex</artifactId>
+            <version>0.11</version>
+            <scope>runtime</scope>
+            <type>jar</type>
+        </dependency>
+        <dependency>
+            <groupId>log4j</groupId>
+            <artifactId>log4j</artifactId>
+            <version>1.2.17</version>
+        </dependency>
     </dependencies>
+    <build>
+	<plugins>
+		<plugin>
+			<artifactId>maven-assembly-plugin</artifactId>
+			<configuration>
+				<archive>
+					<manifest>
+						<mainClass>org.rappsilber.fdr.gui.FDRGUI</mainClass>
+					</manifest>
+				</archive>
+				<descriptorRefs>
+					<descriptorRef>jar-with-dependencies</descriptorRef>
+				</descriptorRefs>
+			</configuration>
+		</plugin>		
+	</plugins>
+    </build>
+
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <maven.compiler.source>1.7</maven.compiler.source>
         <maven.compiler.target>1.7</maven.compiler.target>
     </properties>
-</project>
\ No newline at end of file
+</project>