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