Ant script should now work outside the eclipse environment

build.properties

@@ -3,6 +3,7 @@ src.dir=Source
 classes.dir=Classes
 orig.doc.dir=Documentation/USeqDocumentation
 base.dir=Releases
+library.jar=LibraryJars
 release.name=USeq_${version}
 release.base.dir=${base.dir}/${release.name}
 release.build.dir=${release.base.dir}/build

build.xml

@@ -7,6 +7,7 @@
 	<target name="clean">
 		<delete dir="${release.base.dir}"/>
 	</target>
+
 
 	<target name="master-jar" description="creates the master jar file with all code" depends="clean">
 
@@ -22,6 +23,17 @@
 		<delete dir="${release.build.dir}/__MACOSX"/>
 		<delete file="${release.build.dir}/JavaxComOrgInfoNetClasses.zip"/>
 
+
+		<javac srcdir="${src.dir}" destdir="${classes.dir}">
+			 <exclude name="**/AutoNovoaligner.java"/>
+			 <exclude name="**/SNPComparator.java"/>
+			   <classpath>
+			   		<fileset dir="${release.build.dir}" includes="**/*jar"/>
+			   		<fileset dir="${library.jar}" includes="**/*jar"/>
+			   </classpath>
+		</javac>
+
+
 		<!-- Copy Driver -->
 		<macrodef name="copy-class">
 			<attribute name="jarpath"/>
@@ -210,11 +222,11 @@
 		<echo>Creating Symlink to the applications in home</echo>
 		<symlink link="/Users/timmosbruger/AppsUSeq" resource="/Users/timmosbruger/Documents/eclipse4.3/USeq/Releases/${release.name}/Apps/"/>
 		<echo>Copying applications to server</echo>
-		<exec executable="rsync" dir="/Users/timmosbruger/Documents/eclipse4.3/USeq/Releases/">
+<!--		<exec executable="rsync" dir="/Users/timmosbruger/Documents/eclipse4.3/USeq/Releases/">
 			<arg value="-r"/>
 			<arg value="${release.name}"/>
 			<arg value="${env.moab}:/home/u0855942/tim_scripts/"/>
-		</exec>
+		</exec> -->
 	</target>
 
 	<target name="nix-release" depends="build-release">