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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>
|
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