From a0be74c2ef145ca784691cf7bdc33ae260c23cf7 Mon Sep 17 00:00:00 2001
From: David Roazen <droazen@broadinstitute.org>
Date: Fri, 1 Mar 2013 15:33:59 -0500
Subject: [PATCH] Ant target to package a GATK jar with private included

Needed before we can start emitting full unstable jars from
Bamboo for our internal use.
---
 build.xml | 15 ++++++++++++---
 1 file changed, 12 insertions(+), 3 deletions(-)

diff --git a/build.xml b/build.xml
index 2555227dc..03f3232f2 100644
--- a/build.xml
+++ b/build.xml
@@ -865,14 +865,18 @@
         <property name="executable" value="GenomeAnalysisTK" />
     </target>
 
-    <target name="init.executable.queueall" depends="init.build.all, init.javaandscala">
-        <property name="executable" value="Queue" />
+    <target name="init.executable.gatkall" depends="init.build.all, init.javaonly">
+        <property name="executable" value="GenomeAnalysisTK" />
     </target>
 
     <target name="init.executable.queuefull" depends="init.build.publicprotectedonly, init.javaandscala">
         <property name="executable" value="Queue" />
     </target>
 
+    <target name="init.executable.queueall" depends="init.build.all, init.javaandscala">
+        <property name="executable" value="Queue" />
+    </target>
+
     <target name="require.executable">
         <condition property="no.executable.defined">
             <or>
@@ -921,12 +925,17 @@
     </target>
 
     <!-- Package specific versions of the GATK/Queue. ALWAYS do an ant clean before invoking these! -->
+
+    <!-- GATK "full" == public + protected, ie., the standard binary release of the GATK  -->
     <target name="package.gatk.full" depends="init.executable.gatkfull,package" />
 
-    <target name="package.queue.all" depends="init.executable.queueall,package" />
+    <!-- GATK "all" == public + protected + private. Should never be publicly released -->
+    <target name="package.gatk.all" depends="init.executable.gatkall,package" />
 
     <target name="package.queue.full" depends="init.executable.queuefull,package" />
 
+    <target name="package.queue.all" depends="init.executable.queueall,package" />
+
     <!-- Release a build. Don't call this target directly. Call one of the specific release targets below -->
     <target name="release" depends="require.executable" description="release a build, putting each file in a location specified by the package">
         <ant antfile="${package.output.dir}/${executable}.xml" target="release" />