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Merge pull request broadinstitute#533 from broadinstitute/jc_gradle_c…
…ompat Added gradle build compatibility to picard public. This requires a me…
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@@ -41,7 +41,7 @@ | |
<property name="htsjdk_lib_dir" value="${dist}/htsjdk_lib_dir"/> | ||
<property name="htsjdk_git_url" value="[email protected]:samtools/htsjdk.git"/> | ||
<!-- TODO: get this from the build.xml in htsjdk --> | ||
<property name="htsjdk-classes" value="htsjdk/classes"/> | ||
<property name="htsjdk-classes" value="htsjdk/build/classes/main"/> | ||
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<property name="javac.target" value="1.8"/> | ||
<property name="javac.debug" value="true"/> | ||
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@@ -61,15 +61,20 @@ | |
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<property environment="env"/> | ||
<property name="htsjdk" value="htsjdk"/> | ||
<property name="htsjdk_src" value="${htsjdk}/src/java"/> | ||
<property name="htsjdk_src" value="${htsjdk}/src/main/java"/> | ||
<property name="jar_opt" value=".jar_opt"/> | ||
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<property name="gradle.executable" location="${htsjdk}/gradlew"/> | ||
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<property name="htsjdk-version-file" value="${htsjdk}/htsjdk.version.properties"/> | ||
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<condition property="isUnix"> | ||
<os family="unix"/> | ||
</condition> | ||
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<!-- Import JaCoCo Ant tasks --> | ||
<taskdef uri="antlib:org.jacoco.ant" resource="org/jacoco/ant/antlib.xml"> | ||
<classpath path="lib/ant/jacocoant.jar" /> | ||
<classpath path="lib/ant/jacocoant.jar"/> | ||
</taskdef> | ||
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<target name="set_excluded_test_groups_unix" if="isUnix"> | ||
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@@ -87,19 +92,14 @@ | |
<include name="*.jar"/> | ||
<include name="**/*.jar"/> | ||
</fileset> | ||
<!-- for the specific HTSJDK library JARs --> | ||
<fileset dir="${htsjdk}/lib"> | ||
<include name="*.jar"/> | ||
<include name="**/*.jar"/> | ||
</fileset> | ||
<fileset dir="${lib}"> | ||
<include name="**/*.jar"/> | ||
</fileset> | ||
</path> | ||
<path id="metrics.classpath"> | ||
<pathelement path="${classpath}"/> | ||
<pathelement location="${classes}"/> | ||
<pathelement location="${htsjdk}/classes"/> | ||
<pathelement location="${htsjdk}/build/classes/main"/> | ||
</path> | ||
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</target> | ||
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@@ -116,10 +116,9 @@ | |
<target name="clean" description="Clean local build products and also nested project" depends="clean-local, clean-htsjdk"/> | ||
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<!-- HTS-JDK --> | ||
<target name="set-htsjdk-version"> | ||
<target name="set-htsjdk-version" depends="write-version-property"> | ||
<!-- set the htsjdk version --> | ||
<ant antfile="build.xml" dir="${htsjdk}" target="write-version-property" inheritall="false"/> | ||
<loadfile property="htsjdk-version" srcFile="${htsjdk}/htsjdk.version.properties"> | ||
<loadfile property="htsjdk-version" srcFile="${htsjdk-version-file}"> | ||
<filterchain> | ||
<linecontains> | ||
<contains value="htsjdk-version="/> | ||
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@@ -132,8 +131,20 @@ | |
</loadfile> | ||
</target> | ||
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<target name="write-version-property"> | ||
<exec outputproperty="htsjdk-version" executable="${gradle.executable}" dir="${htsjdk}"> | ||
<arg value="-q"/> | ||
<arg value="printVersion"/> | ||
</exec> | ||
<propertyfile | ||
file="${htsjdk-version-file}" | ||
comment="htsjdk version"> | ||
<entry key="htsjdk-version" value="${htsjdk-version}"/> | ||
</propertyfile> | ||
</target> | ||
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<target name="clone-htsjdk" description="Clone HTS-JDK sources from Github"> | ||
<exec executable="git" failonerror="true"> | ||
<exec executable="git" failonerror="true"> | ||
<arg value="clone"/> | ||
<arg value="${htsjdk_git_url}"/> | ||
<arg value="${htsjdk}"/> | ||
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@@ -152,33 +163,39 @@ | |
<exec dir="${htsjdk}" executable="git" failonerror="true"> | ||
<arg value="checkout"/> | ||
<arg value="${htsjdk_latest_tag}"/> | ||
</exec> | ||
</exec> | ||
</target> | ||
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<target name="compile-htsjdk" depends="set-htsjdk-version" description="Build HTS-JDK, and grab build jars"> | ||
<ant antfile="build.xml" dir="${htsjdk}" target="clean" inheritall="false"/> | ||
<ant antfile="build.xml" dir="${htsjdk}" target="all" inheritall="false"/> | ||
<exec executable="${gradle.executable}" dir="${htsjdk}"> | ||
<arg value="shadowJar"/> | ||
</exec> | ||
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<copy todir="${htsjdk_lib_dir}"> | ||
<fileset dir="${htsjdk}/dist" includes="**/*-*.jar"/> | ||
<fileset dir="${htsjdk}/lib" includes="*.jar"/> | ||
<fileset dir="${htsjdk}/build/libs" includes="**/*-all.jar"/> | ||
</copy> | ||
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<copy todir="${dist}"> | ||
<fileset dir="${htsjdk}/dist" includes="**/*.jar" excludes="**/*-*.jar"/> | ||
<fileset dir="${htsjdk}/build/libs" includes="**/*.jar" excludes="**/*-*.jar"/> | ||
</copy> | ||
<!-- set the htsjdk version --> | ||
<ant antfile="build.xml" dir="${htsjdk}" target="write-version-property" inheritall="false"/> | ||
</target> | ||
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<target name="clean-htsjdk" description="Clean HTS-JDK"> | ||
<ant antfile="build.xml" dir="${htsjdk}" target="clean" inheritall="false"/> | ||
<exec executable="${gradle.executable}" dir="${htsjdk}"> | ||
<arg value="clean"/> | ||
</exec> | ||
</target> | ||
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<target name="test-htsjdk" description="Test HTS-JDK"> | ||
<ant antfile="build.xml" dir="${htsjdk}" target="test" inheritall="false"/> | ||
<exec executable="${gradle.executable}" dir="${htsjdk}"> | ||
<arg value="test"/> | ||
</exec> | ||
</target> | ||
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<target name="compile-htsjdk-tests" description="Compile HTS-JDK Tests"> | ||
<ant antfile="build.xml" dir="${htsjdk}" target="compile-tests" inheritall="false"/> | ||
<exec executable="${gradle.executable}" dir="${htsjdk}"> | ||
<arg value="testClasses"/> | ||
</exec> | ||
</target> | ||
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<!-- COMPILE --> | ||
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@@ -189,7 +206,7 @@ | |
<target name="compile-src" depends="compile-htsjdk, compile-picard" description="Compile files without cleaning"/> | ||
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<target name="compile-picard" depends="init" description="Compile picard files without cleaning"> | ||
<compile-src includes="picard/**/*.*" /> | ||
<compile-src includes="picard/**/*.*"/> | ||
</target> | ||
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<target name="compile-tests" depends="compile-htsjdk-tests, compile-picard-tests" description="Compile test files without cleaning"/> | ||
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@@ -315,7 +332,7 @@ | |
<jar destfile="${dist}/picard.jar" compress="no"> | ||
<fileset dir="${classes}" includes="picard/**/*.*, META-INF/**/*"/> | ||
<fileset dir="${src.scripts}" includes="**/*.R"/> | ||
<fileset dir="${htsjdk-classes}" includes ="${htsjdk}/*/**/*.*"/> | ||
<fileset dir="${htsjdk-classes}" includes="${htsjdk}/*/**/*.*"/> | ||
<fileset dir="${dist.tmp}" includes="**/*"/> | ||
<fileset dir="${jar_opt}" includes="**/*"/> | ||
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@@ -345,7 +362,7 @@ | |
</jar> | ||
</target> | ||
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<target name="javadoc" depends="init" description="Generates the project javadoc."> | ||
<target name="javadoc" depends="init, compile, compile-htsjdk" description="Generates the project javadoc."> | ||
<javadoc | ||
destdir="javadoc/picard" | ||
packagenames="picard*" | ||
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@@ -363,11 +380,10 @@ | |
<fileset dir="${lib}"> | ||
<include name="**/*.jar"/> | ||
</fileset> | ||
<fileset dir="${htsjdk}/dist"> | ||
<include name="**/*.jar"/> | ||
</fileset> | ||
<fileset dir="${htsjdk}/lib"> | ||
<include name="**/*.jar"/> | ||
<fileset dir="${htsjdk}/build/libs"> | ||
<include name="**/*-all.jar"/> | ||
<exclude name="**/*-sources.jar"/> | ||
<exclude name="**/*-javadoc.jar"/> | ||
</fileset> | ||
</classpath> | ||
<link href="http://java.sun.com/j2se/1.6.0/docs/api/"/> | ||
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@@ -392,8 +408,10 @@ | |
<fileset dir="${lib}"> | ||
<include name="**/*.jar"/> | ||
</fileset> | ||
<fileset dir="${htsjdk}/lib"> | ||
<fileset dir="${htsjdk}/build/libs"> | ||
<include name="**/*.jar"/> | ||
<exclude name="**/*-sources.jar"/> | ||
<exclude name="**/*-javadoc.jar"/> | ||
</fileset> | ||
</classpath> | ||
<link href="http://java.sun.com/j2se/1.6.0/docs/api/"/> | ||
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@@ -411,8 +429,10 @@ | |
<fileset dir="${lib}"> | ||
<include name="**/*.jar"/> | ||
</fileset> | ||
<fileset dir="${htsjdk}/dist"> | ||
<fileset dir="${htsjdk}/build/libs"> | ||
<include name="**/*.jar"/> | ||
<exclude name="**/*-sources.jar"/> | ||
<exclude name="**/*-javadoc.jar"/> | ||
</fileset> | ||
</classpath> | ||
<fileset dir="."> | ||
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@@ -427,7 +447,7 @@ | |
<property name="addGATKToolsJava" value="1"/> | ||
</target> | ||
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<target name="package-commands-ga4gh" depends="add-ga4gh-support, compile, picard-jar" /> | ||
<target name="package-commands-ga4gh" depends="add-ga4gh-support, compile, picard-jar"/> | ||
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<target name="package-commands" depends="compile, picard-jar"> | ||
<delete dir="${command-line-html-dir}"/> | ||
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@@ -545,10 +565,10 @@ | |
<java classname="picard.cmdline.CreateHtmlDocForStandardOptions" | ||
output="${command-line-html-dir}/program_usage/standard-options.html" | ||
failonerror="true"> | ||
<classpath> | ||
<path refid="classpath"/> | ||
<pathelement location="${classes}"/> | ||
</classpath> | ||
<classpath> | ||
<path refid="classpath"/> | ||
<pathelement location="${classes}"/> | ||
</classpath> | ||
</java> | ||
</sequential> | ||
</target> | ||
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@@ -567,10 +587,10 @@ | |
<java classname="picard.cmdline.CreateHtmlDocForProgram" | ||
output="${command-line-html-dir}/program_usage/@{title}.html" | ||
failonerror="true"> | ||
<classpath> | ||
<path refid="classpath"/> | ||
<pathelement location="${classes}"/> | ||
</classpath> | ||
<classpath> | ||
<path refid="classpath"/> | ||
<pathelement location="${classes}"/> | ||
</classpath> | ||
<arg value="@{main-class}"/> | ||
</java> | ||
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