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Bug fixes for build.xml related to the public/private restructuring.

This commit is contained in:
David Roazen 2011-06-28 12:55:18 -04:00
parent 139c6b84a1
commit 7e243fae6e
1 changed files with 47 additions and 21 deletions
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54
build.xml
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@ -91,11 +91,9 @@
<!-- the path for resources that need to go into the GATK jar; <!-- the path for resources that need to go into the GATK jar;
any additional resources should go into this set. --> any additional resources should go into this set. -->
<path id="gatk.resources"> <path id="gatk.resources">
<fileset dir="${java.public.source.dir}"> <fileset dir="${basedir}">
<include name="**/**/templates/*" /> <include name="${java.public.source.dir}/**/templates/*" />
</fileset> <include name="${java.private.source.dir}/**/templates/*" if="include.private" />
<fileset dir="${java.private.source.dir}">
<include name="**/**/templates/*" />
</fileset> </fileset>
</path> </path>
@ -264,18 +262,19 @@
</taskdef> </taskdef>
</target> </target>
<target name="gatk.compile.source" depends="tribble,init,resolve" <target name="gatk.compile.public.source" depends="tribble,init,resolve">
description="compile the source">
<!-- Compile the java code from ${src} into build -->
<javac fork="true" srcdir="${java.public.source.dir}" memoryMaximumSize="512m" destdir="${java.classes}" debug="true" debuglevel="lines,vars,source" classpathref="external.dependencies" tempdir="${java.io.tmpdir}"> <javac fork="true" srcdir="${java.public.source.dir}" memoryMaximumSize="512m" destdir="${java.classes}" debug="true" debuglevel="lines,vars,source" classpathref="external.dependencies" tempdir="${java.io.tmpdir}">
<compilerarg value="-proc:none"/> <compilerarg value="-proc:none"/>
</javac> </javac>
</target>
<target name="gatk.compile.private.source" depends="gatk.compile.public.source" if="include.private">
<javac fork="true" srcdir="${java.private.source.dir}" memoryMaximumSize="512m" destdir="${java.classes}" debug="true" debuglevel="lines,vars,source" classpathref="external.dependencies" tempdir="${java.io.tmpdir}"> <javac fork="true" srcdir="${java.private.source.dir}" memoryMaximumSize="512m" destdir="${java.classes}" debug="true" debuglevel="lines,vars,source" classpathref="external.dependencies" tempdir="${java.io.tmpdir}">
<exclude name="**" unless="include.private" />
<compilerarg value="-proc:none"/> <compilerarg value="-proc:none"/>
</javac> </javac>
</target>
<target name="gatk.compile.external.source" depends="gatk.compile.public.source,gatk.compile.private.source">
<subant target="compile" genericantfile="build.xml"> <subant target="compile" genericantfile="build.xml">
<property name="build.dir" value="${external.build.dir}" /> <property name="build.dir" value="${external.build.dir}" />
<property name="dist.dir" value="${external.dist.dir}" /> <property name="dist.dir" value="${external.dist.dir}" />
@ -284,7 +283,11 @@
</subant> </subant>
</target> </target>
<target name="gatk.contracts" depends="gatk.compile.source" description="create GATK contracts" if="use.contracts"> <target name="gatk.compile.source"
depends="gatk.compile.public.source,gatk.compile.private.source,gatk.compile.external.source"
description="compile the GATK source" />
<target name="gatk.contracts.public" depends="gatk.compile.source">
<javac fork="true" memoryMaximumSize="512m" srcdir="${java.public.source.dir}" destdir="${java.contracts}" debug="true" debuglevel="lines,vars,source" tempdir="${java.io.tmpdir}" > <javac fork="true" memoryMaximumSize="512m" srcdir="${java.public.source.dir}" destdir="${java.contracts}" debug="true" debuglevel="lines,vars,source" tempdir="${java.io.tmpdir}" >
<classpath> <classpath>
<path refid="external.dependencies" /> <path refid="external.dependencies" />
@ -294,8 +297,10 @@
<compilerarg value="-Acom.google.java.contract.dump=dump/"/> <compilerarg value="-Acom.google.java.contract.dump=dump/"/>
<compilerarg value="-proc:only"/> <compilerarg value="-proc:only"/>
</javac> </javac>
</target>
<target name="gatk.contracts.private" depends="gatk.compile.source" if="include.private">
<javac fork="true" memoryMaximumSize="512m" srcdir="${java.private.source.dir}" destdir="${java.contracts}" debug="true" debuglevel="lines,vars,source" tempdir="${java.io.tmpdir}" > <javac fork="true" memoryMaximumSize="512m" srcdir="${java.private.source.dir}" destdir="${java.contracts}" debug="true" debuglevel="lines,vars,source" tempdir="${java.io.tmpdir}" >
<exclude name="**" unless="include.private" />
<classpath> <classpath>
<path refid="external.dependencies" /> <path refid="external.dependencies" />
<pathelement path="${java.classes}" /> <pathelement path="${java.classes}" />
@ -306,6 +311,9 @@
</javac> </javac>
</target> </target>
<target name="gatk.contracts" depends="gatk.contracts.public,gatk.contracts.private"
description="create GATK contracts" if="use.contracts" />
<target name="gatk.compile" depends="tribble,init,resolve,gatk.compile.source,gatk.contracts" /> <target name="gatk.compile" depends="tribble,init,resolve,gatk.compile.source,gatk.contracts" />
<target name="init.queue-extensions.generate" depends="gatk.compile"> <target name="init.queue-extensions.generate" depends="gatk.compile">
@ -342,18 +350,36 @@
</target> </target>
<!-- Scala depends on the java compile --> <!-- Scala depends on the java compile -->
<target name="scala.compile" depends="init,resolve,gatk.compile,queue-extensions.generate,init.scala.compile" if="scala.include" description="compile Scala"> <target name="scala.compile.public" depends="init,resolve,gatk.compile,queue-extensions.generate,init.scala.compile" if="scala.include">
<mkdir dir="${scala.classes}"/> <mkdir dir="${scala.classes}"/>
<echo>Building Scala...</echo> <echo>Building Scala...</echo>
<scalac fork="true" jvmargs="-Xmx512m" destdir="${scala.classes}" classpathref="scala.dependencies" deprecation="yes" unchecked="yes"> <scalac fork="true" jvmargs="-Xmx512m" destdir="${scala.classes}" classpathref="scala.dependencies" deprecation="yes" unchecked="yes">
<src path="${scala.public.source.dir}" /> <src path="${scala.public.source.dir}" />
<src path="${scala.private.source.dir}" />
<src path="${queue-extensions.source.dir}" /> <src path="${queue-extensions.source.dir}" />
<include name="**/*.scala"/> <include name="**/*.scala"/>
<exclude name="**/gridengine/**" unless="include.gridengine" /> <exclude name="**/gridengine/**" unless="include.gridengine" />
</scalac> </scalac>
</target> </target>
<target name="check.scala.private" depends="scala.compile.public">
<condition property="include.scala.private">
<and>
<isset property="include.private" />
<isset property="scala.include" />
</and>
</condition>
</target>
<target name="scala.compile.private" depends="check.scala.private" if="include.scala.private">
<scalac fork="true" jvmargs="-Xmx512m" destdir="${scala.classes}" classpathref="scala.dependencies" deprecation="yes" unchecked="yes">
<src path="${scala.private.source.dir}" />
<include name="**/*.scala"/>
<exclude name="**/gridengine/**" unless="include.gridengine" />
</scalac>
</target>
<target name="scala.compile" depends="scala.compile.public,scala.compile.private" if="scala.include" description="compile Scala" />
<target name="init.extracthelp" depends="gatk.compile"> <target name="init.extracthelp" depends="gatk.compile">
<loadfile property="properties.version" srcfile="${basedir}/${resource.path}" failonerror="false" quiet="true"> <loadfile property="properties.version" srcfile="${basedir}/${resource.path}" failonerror="false" quiet="true">
<filterchain> <filterchain>
@ -652,7 +678,7 @@
<antcall target="resolve"> <antcall target="resolve">
<param name="ivy.conf" value="test"/> <param name="ivy.conf" value="test"/>
</antcall> </antcall>
<scalac fork="true" jvmargs="-Xmx512m" srcdir="${scala.test.sources}" destdir="${scala.test.classes}" deprecation="yes" unchecked="yes"> <scalac fork="true" jvmargs="-Xmx512m" destdir="${scala.test.classes}" deprecation="yes" unchecked="yes">
<src path="${scala.public.test.sources}" /> <src path="${scala.public.test.sources}" />
<src path="${scala.private.test.sources}" /> <src path="${scala.private.test.sources}" />
<include name="**/*.scala"/> <include name="**/*.scala"/>