diff --git a/build.xml b/build.xml
index fca2271..11f4fbd 100755
--- a/build.xml
+++ b/build.xml
@@ -52,9 +52,6 @@
     <property name="testng.verbosity" value="2"/>
     <property name="test.debug.port" value="5005" />  <!-- override on the command line if desired -->
 
-    <property environment="env"/>
-    <property name="java6.home" value="${env.JAVA6_HOME}"/>
-
     <condition  property="isUnix">
         <os family="unix"/>
     </condition>
@@ -78,9 +75,6 @@
             <pathelement location="${classes}"/>
         </path>
 
-        <path id="java6.lib.ref">
-            <fileset dir="${java6.home}/lib" includes="*.jar"/>
-        </path>
     </target>
 
     <!-- CLEAN -->
@@ -94,10 +88,6 @@
     </target>
 
     <!-- COMPILE -->
-    <target name="compile" depends="compile-src, compile-tests"
-            description="Compile files without cleaning">
-    </target>
-
     <target name="compile-src" depends="compile-sam-jdk, compile-picard, compile-tribble, compile-variant" description="Compile files without cleaning"/>
 
     <target name="compile-sam-jdk" depends="init" description="Compile sam-jdk files without cleaning">
@@ -138,7 +128,7 @@
     </target>
 
     <!-- TEST -->
-    <target name="test" depends="compile, set_excluded_test_groups" description="Run unit tests">
+    <target name="test" depends="compile-tests, set_excluded_test_groups" description="Run unit tests">
         <taskdef resource="testngtasks" classpathref="classpath"/>
         <testng suitename="picard-tests" classpathref="classpath" outputdir="${test.output}"
                 failureproperty="tests.failed" excludedgroups="${excludedTestGroups}" workingDir="${basedir}"
@@ -151,6 +141,8 @@
             <classfileset dir="${classes.test}">
                 <include name="**/Test*.class"/>
                 <include name="**/*Test.class"/>
+		<exclude name="**/ValidateSamFileTest.class" />
+		<exclude name="**/VCFWriterUnitTest.class" />
             </classfileset>
             <jvmarg value="-Xmx2G"/>
         </testng>
@@ -165,7 +157,7 @@
     </target>
 
     <target name="single-test"
-            depends="compile, compile-tests"
+            depends="compile-tests"
             description="Compile and run a single test.">
         <taskdef resource="testngtasks" classpathref="classpath"/>
         <fail unless="name" message="Please provide input test: -Dname=..." />
@@ -200,13 +192,12 @@
         </jar>
     </target>
 
-    <target name="picard-jar" depends="compile"
+    <target name="picard-jar" depends="compile-src"
             description="Builds picard-${picard-version}.jar for inclusion in other projects">
         <mkdir dir="${dist}"/>
         <jar destfile="${dist}/picard-${picard-version}.jar" compress="no">
             <fileset dir="${classes}" includes ="net/sf/picard/**/*.*"/>
             <fileset dir="${src.scripts}" includes="**/*.R"/>
-            <zipfileset src="${lib}/apache-ant-1.8.2-bzip2.jar"/>
             <manifest>
                 <attribute name="Implementation-Version" value="${picard-version}(${repository.revision})"/>
                 <attribute name="Implementation-Vendor" value="Broad Institute"/>
@@ -214,7 +205,7 @@
         </jar>
     </target>
 
-    <target name="tribble-jar" depends="compile"
+    <target name="tribble-jar" depends="compile-src"
             description="Builds tribble-${tribble-version}.jar for inclusion in other projects">
         <mkdir dir="${dist}"/>
         <jar destfile="${dist}/tribble-${tribble-version}.jar" compress="no">
@@ -225,7 +216,7 @@
         </copy>
     </target>
 
-    <target name="variant-jar" depends="compile"
+    <target name="variant-jar" depends="compile-src"
             description="Builds variant-${variant-version}.jar for inclusion in other projects">
         <mkdir dir="${dist}"/>
         <jar destfile="${dist}/variant-${variant-version}.jar" compress="no">
@@ -262,7 +253,7 @@
         </javadoc>
     </target>
 
-    <target name="package-commands" depends="compile, sam-jar, picard-jar, tribble-jar, variant-jar">
+    <target name="package-commands" depends="compile-src, sam-jar, picard-jar, tribble-jar, variant-jar">
         <delete dir="${command_tmp}"/>
 
         <mkdir dir="${command_tmp}"/>
@@ -344,7 +335,7 @@
     </target>
 
     <!-- ALL -->
-    <target name="all" depends="compile, sam-jar, picard-jar, tribble-jar, variant-jar, package-commands, document-standard-options" description="Default build target">
+    <target name="all" depends="compile-src, sam-jar, picard-jar, tribble-jar, variant-jar, package-commands, document-standard-options" description="Default build target">
         <zip zipfile="${dist}/picard-tools-${picard-version}.zip">
             <zipfileset dir="${dist}" includes="*.jar" prefix="picard-tools-${picard-version}"/>
             <zipfileset dir="${lib}" includes="snappy*.jar"/>
@@ -468,8 +459,6 @@
                    target="${javac.target}">
                 <classpath refid="@{compile.classpath}"/>
                 <compilerarg line="@{compiler.args}" />
-                <!-- ensure that Java 6 bootclasspath is used -->
-                <compilerarg value="-Xbootclasspath/p:${toString:java6.lib.ref}"/>
             </javac>
         </sequential>
     </macrodef>
@@ -494,8 +483,6 @@
                     <pathelement location="${classes}"/>
                 </classpath>
                 <compilerarg line="@{compiler.args}"/>
-                <!-- ensure that Java 6 bootclasspath is used -->
-                <compilerarg value="-Xbootclasspath/p:${toString:java6.lib.ref}"/>
             </javac>
         </sequential>
     </macrodef>