From d770122611811effcf18a2c53cc46f65c8781c37 Mon Sep 17 00:00:00 2001
From: Olof Olsson <borsna@gmail.com>
Date: Wed, 6 Aug 2014 21:24:17 +0200
Subject: [PATCH 1/2] added build with all dependencies included

builds a jar with all the dependent libraries included for easier depployment
---
 pom.xml | 31 +++++++++++++++++++++----------
 1 file changed, 21 insertions(+), 10 deletions(-)

diff --git a/pom.xml b/pom.xml
index 11946b1..c8b3a72 100644
--- a/pom.xml
+++ b/pom.xml
@@ -132,19 +132,30 @@
         </configuration>
       </plugin>
       <plugin>
-	<groupId>org.apache.maven.plugins</groupId>
-	<artifactId>maven-assembly-plugin</artifactId>
-	<version>2.4</version>
-	<configuration>
-	  <appendAssemblyId>false</appendAssemblyId>
-	  <descriptors>
-	    <descriptor>package.xml</descriptor>
-	  </descriptors>
-	</configuration>
+        <groupId>org.apache.maven.plugins</groupId>
+        <artifactId>maven-assembly-plugin</artifactId>
+        <version>2.4</version>
+        <configuration>
+          <descriptorRefs>
+          <descriptorRef>jar-with-dependencies</descriptorRef>
+          </descriptorRefs>
+          <archive>
+            <manifest>
+              <mainClass>nl.mpi.mdmapper.Main</mainClass>
+            </manifest>
+          </archive>
+        </configuration>
+        <executions>
+          <execution>
+            <phase>package</phase>
+            <goals>
+              <goal>single</goal>
+            </goals>
+          </execution>
+        </executions>				
       </plugin>
     </plugins>
   </build>
-
   <reporting>
     <plugins>
       <plugin>

From 198284323bc586d3228661fa4d4440c23229a1c4 Mon Sep 17 00:00:00 2001
From: Olof Olsson <borsna@gmail.com>
Date: Wed, 6 Aug 2014 21:26:43 +0200
Subject: [PATCH 2/2] fix for classpath when using -jar

If -jar argument is given classpath given by -cp is ignored, this is a fix for this issue
---
 src/main/scripts/run-mapper.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/scripts/run-mapper.sh b/src/main/scripts/run-mapper.sh
index 1a1fb8f..1bdec61 100755
--- a/src/main/scripts/run-mapper.sh
+++ b/src/main/scripts/run-mapper.sh
@@ -9,4 +9,4 @@ for x in lib/*.jar ; do
   y=${y}:${x}
 done
 
-nice java -cp ${y} -jar ${JAR} mapper_version=${mapper_version} $*
+nice java -cp ${y}:${JAR} nl.mpi.mdmapper.Main mapper_version=${mapper_version} $*