From 4dfed62e7d18b73646a9028fd75bfb3660f57749 Mon Sep 17 00:00:00 2001
From: kshakir <kshakir@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 4 Oct 2010 19:38:29 +0000
Subject: [PATCH] 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
---
 build.xml | 42 +++++++++++++-----------------------------
 1 file changed, 13 insertions(+), 29 deletions(-)

diff --git a/build.xml b/build.xml
index be21ff8d2..35cc89f44 100644
--- a/build.xml
+++ b/build.xml
@@ -14,7 +14,6 @@
     <property name="queue.classes" value="${build.dir}/scala/classes" />
 
     <property name="queue-extensions.source.dir" value="${build.dir}/queue-extensions/src" />
-    <property name="queue-extensions.classes" value="${build.dir}/queue-extensions/classes" />
     
     <!-- where to find the tribble distro -->
     <property name="tribble.dir" value="tribble" />
@@ -78,13 +77,6 @@
     <path id="queue.dependencies">
         <path refid="external.dependencies" />
         <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="${queue.classes}" />
         <!-- Need the resources as we will be running a command line program which needs the help text. -->
         <pathelement location="${resource.path}" />
     </path>
@@ -227,20 +219,11 @@
         </subant>
     </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="${queue.classes}" classpathref="queue.dependencies" deprecation="yes" unchecked="yes">
-            <include name="org/broadinstitute/sting/queue/**/*.scala"/>
-        </scalac>
-    </target>
-
     <!-- NOTE: Extracting help first to avoid "Unable to load help text.  Help output will be sparse." warning message. -->
-    <target name="queue-extensions.generate" depends="gatk.compile, queue.compile, extracthelp" if="queue.include" description="generate GATK modules for Queue">
+    <target name="queue-extensions.generate" depends="gatk.compile, extracthelp" if="queue.include" description="generate GATK modules for Queue">
         <mkdir dir="${queue-extensions.source.dir}"/>
         <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 path="${queue-extensions.source.dir}" />
             <arg value="-l" />
@@ -248,11 +231,15 @@
         </java>
     </target>
 
-    <target name="queue-extensions.compile" depends="queue-extensions.generate" if="queue.include" description="compile extensions for Queue">
-        <mkdir dir="${queue-extensions.classes}"/>
-        <echo>Building Queue GATK extensions...</echo>
-        <scalac srcdir="${queue-extensions.source.dir}" destdir="${queue-extensions.classes}" classpathref="queue-extensions.dependencies" deprecation="yes" unchecked="yes">
+    <!-- Queue depends on the gatk since it contains the StingUtils (including CommandLine) -->
+    <target name="queue.compile" depends="init,resolve,gatk.compile,init.scalatasks,queue-extensions.generate" if="queue.include" description="compile Queue">
+        <mkdir dir="${queue.classes}"/>
+        <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"/>
+            <exclude name="*.scala"/>
         </scalac>
     </target>
 
@@ -273,7 +260,7 @@
       </javadoc>
     </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">
         <mkdir dir="${dist.dir}"/>
@@ -326,7 +313,7 @@
 
     </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="${dist.dir}/Queue.jar">
             <fileset dir="${queue.classes}">
                 <include name="org/broadinstitute/sting/queue/**/*.class"/>
@@ -334,9 +321,6 @@
             <fileset dir="${java.classes}">
               <include name="org/broadinstitute/sting/queue/**/*.class" />
             </fileset>
-            <fileset dir="${queue-extensions.classes}">
-              <include name="**/*.class" />
-            </fileset>
             <manifest>
                 <attribute name="Main-Class" value="org.broadinstitute.sting.queue.QCommandLine" />
             </manifest>
@@ -587,7 +571,7 @@
       </javadoc>
 
         <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-extensions.source.dir}"/>
             <include name="org/broadinstitute/sting/queue/**/*.scala"/>