diff --git a/build.xml b/build.xml
index dbdafa3d9..ffb564cd2 100644
--- a/build.xml
+++ b/build.xml
@@ -281,6 +281,10 @@
         <equals arg1="${gatk.target}" arg2="private" casesensitive="false" />
       </condition>
 
+      <condition property="include.external">
+          <available file="${external.dir}"/>
+      </condition>
+
       <condition property="include.contracts">
         <equals arg1="${use.contracts}" arg2="true" />
       </condition>
@@ -331,7 +335,7 @@
         </javac>
     </target>
 
-    <target name="gatk.compile.external.source" depends="gatk.compile.public.source,gatk.compile.private.source">
+    <target name="gatk.compile.external.source" depends="gatk.compile.public.source,gatk.compile.private.source" if="include.external">
         <subant target="compile" genericantfile="build.xml">
             <property name="build.dir" value="${external.build.dir}" />
             <property name="dist.dir" value="${external.dist.dir}" />
@@ -761,6 +765,7 @@
     <property name="java.test.classes" value="${build.dir}/java/testclasses"/>
     <property name="java.public.test.classes" value="${java.test.classes}/public"/>
     <property name="java.private.test.classes" value="${java.test.classes}/private"/>
+    <property name="java.external.test.classes" value="${java.test.classes}/external"/>
     <property name="java.public.test.sources" value="${public.dir}/java/test"/>
     <property name="java.private.test.sources" value="${private.dir}/java/test"/>
     <property name="scala.test.classes" value="${build.dir}/scala/testclasses"/>
@@ -811,7 +816,23 @@
         </javac>
     </target>
 
-    <target name="test.java.compile" depends="test.java.public.compile, test.java.private.compile"/>
+    <target name="test.java.external.compile" depends="dist,test.init.compile,test.java.public.compile" if="include.external">
+        <mkdir dir="${java.external.test.classes}"/>
+        <echo message="Sting: Compiling external test cases!"/>
+        <javac fork="true" memoryMaximumSize="512m" destdir="${java.external.test.classes}" debug="true" optimize="on" tempdir="${java.io.tmpdir}" srcdir="${external.dir}">
+            <include name="*/test/**/*.java"/>
+            <classpath>
+                <path refid="external.dependencies" />
+                <pathelement location="${java.public.test.classes}"/>
+                <pathelement location="${java.classes}"/>
+                <pathelement location="${java.contracts}"/>
+                <pathelement location="${testng.jar}"/>
+            </classpath>
+            <compilerarg value="-proc:none"/>
+        </javac>
+    </target>
+
+    <target name="test.java.compile" depends="test.java.public.compile, test.java.private.compile, test.java.external.compile"/>
 
     <target name="test.scala.public.compile" depends="test.java.compile,scala.compile" if="scala.include">
         <mkdir dir="${scala.public.test.classes}"/>
@@ -852,6 +873,7 @@
         <pathelement location="${java.contracts}" />
         <pathelement location="${java.public.test.classes}" />
         <pathelement location="${java.private.test.classes}" />
+        <pathelement location="${java.external.test.classes}" />
         <pathelement location="${scala.public.test.classes}" />
         <pathelement location="${scala.private.test.classes}" />
         <pathelement location="${R.tar.dir}" />
@@ -934,6 +956,9 @@
                 <classfileset dir="${java.private.test.classes}" erroronmissingdir="false">
                     <include name="**/@{testtype}.class" if="include.private"/>
                 </classfileset>
+                <classfileset dir="${java.external.test.classes}" erroronmissingdir="false">
+                    <include name="**/@{testtype}.class" if="include.external"/>
+                </classfileset>
                 <classfileset dir="${scala.public.test.classes}" erroronmissingdir="false">
                     <include name="**/@{testtype}*.class" if="scala.include"/>
                 </classfileset>