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Generating the Queue GATK extensions using java, then compiling all the Queue scala code at once to allow circular dependencies between existing and generated scala code. 

Will see how this behaves for those using IntelliJ as generated source code will disappear during an ant clean.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4425 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kshakir 2010-10-04 19:38:29 +00:00
parent 24cf6f9e36
commit 4dfed62e7d
1 changed files with 13 additions and 29 deletions
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42
build.xml
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@ -14,7 +14,6 @@
<property name="queue.classes" value="${build.dir}/scala/classes" /> <property name="queue.classes" value="${build.dir}/scala/classes" />
<property name="queue-extensions.source.dir" value="${build.dir}/queue-extensions/src" /> <property name="queue-extensions.source.dir" value="${build.dir}/queue-extensions/src" />
<property name="queue-extensions.classes" value="${build.dir}/queue-extensions/classes" />
<!-- where to find the tribble distro --> <!-- where to find the tribble distro -->
<property name="tribble.dir" value="tribble" /> <property name="tribble.dir" value="tribble" />
@ -78,13 +77,6 @@
<path id="queue.dependencies"> <path id="queue.dependencies">
<path refid="external.dependencies" /> <path refid="external.dependencies" />
<pathelement location="${java.classes}" /> <pathelement location="${java.classes}" />
</path>
<!-- Path to queue-extendsions dependencies. -->
<path id="queue-extensions.dependencies">
<path refid="external.dependencies" />
<pathelement location="${java.classes}" />
<pathelement location="${queue.classes}" />
<!-- Need the resources as we will be running a command line program which needs the help text. --> <!-- Need the resources as we will be running a command line program which needs the help text. -->
<pathelement location="${resource.path}" /> <pathelement location="${resource.path}" />
</path> </path>
@ -227,20 +219,11 @@
</subant> </subant>
</target> </target>
<!-- Queue depends on the gatk since it contains the StingUtils (including CommandLine) -->
<target name="queue.compile" depends="init,resolve,gatk.compile,init.scalatasks" if="queue.include" description="build Queue">
<mkdir dir="${queue.classes}"/>
<echo>Building Queue...</echo>
<scalac srcdir="${queue.source.dir}" destdir="${queue.classes}" classpathref="queue.dependencies" deprecation="yes" unchecked="yes">
<include name="org/broadinstitute/sting/queue/**/*.scala"/>
</scalac>
</target>
<!-- NOTE: Extracting help first to avoid "Unable to load help text. Help output will be sparse." warning message. --> <!-- NOTE: Extracting help first to avoid "Unable to load help text. Help output will be sparse." warning message. -->
<target name="queue-extensions.generate" depends="gatk.compile, queue.compile, extracthelp" if="queue.include" description="generate GATK modules for Queue"> <target name="queue-extensions.generate" depends="gatk.compile, extracthelp" if="queue.include" description="generate GATK modules for Queue">
<mkdir dir="${queue-extensions.source.dir}"/> <mkdir dir="${queue-extensions.source.dir}"/>
<echo>Generating Queue GATK extensions...</echo> <echo>Generating Queue GATK extensions...</echo>
<java fork="true" failonerror="true" classname="org.broadinstitute.sting.queue.extensions.gatk.GATKExtensionsGenerator" classpathref="queue-extensions.dependencies"> <java fork="true" failonerror="true" classname="org.broadinstitute.sting.queue.extensions.gatk.GATKExtensionsGenerator" classpathref="queue.dependencies">
<arg value="-outDir" /> <arg value="-outDir" />
<arg path="${queue-extensions.source.dir}" /> <arg path="${queue-extensions.source.dir}" />
<arg value="-l" /> <arg value="-l" />
@ -248,11 +231,15 @@
</java> </java>
</target> </target>
<target name="queue-extensions.compile" depends="queue-extensions.generate" if="queue.include" description="compile extensions for Queue"> <!-- Queue depends on the gatk since it contains the StingUtils (including CommandLine) -->
<mkdir dir="${queue-extensions.classes}"/> <target name="queue.compile" depends="init,resolve,gatk.compile,init.scalatasks,queue-extensions.generate" if="queue.include" description="compile Queue">
<echo>Building Queue GATK extensions...</echo> <mkdir dir="${queue.classes}"/>
<scalac srcdir="${queue-extensions.source.dir}" destdir="${queue-extensions.classes}" classpathref="queue-extensions.dependencies" deprecation="yes" unchecked="yes"> <echo>Building Queue...</echo>
<scalac destdir="${queue.classes}" classpathref="queue.dependencies" deprecation="yes" unchecked="yes">
<src path="${queue.source.dir}" />
<src path="${queue-extensions.source.dir}" />
<include name="**/*.scala"/> <include name="**/*.scala"/>
<exclude name="*.scala"/>
</scalac> </scalac>
</target> </target>
@ -273,7 +260,7 @@
</javadoc> </javadoc>
</target> </target>
<target name="sting.compile" depends="gatk.compile, queue.compile, queue-extensions.compile" /> <target name="sting.compile" depends="gatk.compile, queue.compile" />
<target name="init.jar" depends="sting.compile,extracthelp"> <target name="init.jar" depends="sting.compile,extracthelp">
<mkdir dir="${dist.dir}"/> <mkdir dir="${dist.dir}"/>
@ -326,7 +313,7 @@
</target> </target>
<target name="queue.jar" depends="queue.compile, queue-extensions.compile, init.jar" if="queue.include"> <target name="queue.jar" depends="queue.compile, init.jar" if="queue.include">
<jar jarfile="${dist.dir}/Queue.jar"> <jar jarfile="${dist.dir}/Queue.jar">
<fileset dir="${queue.classes}"> <fileset dir="${queue.classes}">
<include name="org/broadinstitute/sting/queue/**/*.class"/> <include name="org/broadinstitute/sting/queue/**/*.class"/>
@ -334,9 +321,6 @@
<fileset dir="${java.classes}"> <fileset dir="${java.classes}">
<include name="org/broadinstitute/sting/queue/**/*.class" /> <include name="org/broadinstitute/sting/queue/**/*.class" />
</fileset> </fileset>
<fileset dir="${queue-extensions.classes}">
<include name="**/*.class" />
</fileset>
<manifest> <manifest>
<attribute name="Main-Class" value="org.broadinstitute.sting.queue.QCommandLine" /> <attribute name="Main-Class" value="org.broadinstitute.sting.queue.QCommandLine" />
</manifest> </manifest>
@ -587,7 +571,7 @@
</javadoc> </javadoc>
<mkdir dir="javadoc/queue"/> <mkdir dir="javadoc/queue"/>
<scaladoc srcdir="" destdir="javadoc/queue" classpathref="queue-extensions.dependencies" deprecation="yes" unchecked="yes"> <scaladoc srcdir="" destdir="javadoc/queue" classpathref="queue.dependencies" deprecation="yes" unchecked="yes">
<src path="${queue.source.dir}"/> <src path="${queue.source.dir}"/>
<src path="${queue-extensions.source.dir}"/> <src path="${queue-extensions.source.dir}"/>
<include name="org/broadinstitute/sting/queue/**/*.scala"/> <include name="org/broadinstitute/sting/queue/**/*.scala"/>