From fa7605c6436dd2e196bf60690b55f0a4a454f783 Mon Sep 17 00:00:00 2001
From: David Roazen <droazen@broadinstitute.org>
Date: Wed, 15 Aug 2012 22:54:13 -0400
Subject: [PATCH] Convert external.build.dir and external.dist.dir back to
 paths

The previous push fixed the external classpath issue but broke external
builds in a new way by changing the above from paths to properties. This
was a mistake, since external builds require absolute, not relative, paths

Thanks to akiezun for the bug report and patch
---
 build.xml | 22 +++++++++++++---------
 1 file changed, 13 insertions(+), 9 deletions(-)

diff --git a/build.xml b/build.xml
index 2ca48c51b..f681ddafa 100644
--- a/build.xml
+++ b/build.xml
@@ -70,10 +70,6 @@
     <property name="R.package.path" value="org/broadinstitute/sting/utils/R" />
     <property name="R.script.staging.dir" value="${build.dir}/R/stage" />
 
-    <!-- Properties used for external builds -->
-    <property name="external.build.dir" value="${java.classes}" />
-    <property name="external.dist.dir" value="${dist.dir}" />
-
     <!-- Packaging system properties -->
     <property name="package.xml.dir" value="${public.dir}/packages" />
     <property name="package.output.dir" value="${dist.dir}/packages" />
@@ -211,6 +207,14 @@
         <include name="**/*.java" />
     </fileset>
 
+    <path id="external.build.dir">
+        <path path="${java.classes}" />
+    </path>
+
+    <path id="external.dist.dir">
+        <path path="${dist.dir}" />
+    </path>
+
     <!-- GATK dependencies consist of 3rd party plugins plus compiled GATK classes -->
     <path id="external.gatk.classpath">
         <path path="${java.classes}"/>
@@ -425,8 +429,8 @@
 
     <target name="gatk.compile.external.source" depends="gatk.compile.internal.source" if="include.external">
         <subant target="compile" genericantfile="build.xml">
-            <property name="build.dir" value="${external.build.dir}" />
-            <property name="dist.dir" value="${external.dist.dir}" />
+            <property name="build.dir" refid="external.build.dir" />
+            <property name="dist.dir" refid="external.dist.dir" />
             <property name="gatk.classpath" refid="external.gatk.classpath" />
             <fileset dir="${external.dir}" includes="*/build.xml" erroronmissingdir="false" />
         </subant>
@@ -675,9 +679,9 @@
         </jar>
 
         <subant target="dist" genericantfile="build.xml">
-            <property name="build.dir" value="${external.build.dir}" />
-            <property name="dist.dir" value="${external.dist.dir}" />
-            <property name="gatk.classpath" value="${external.gatk.classpath}" />
+            <property name="build.dir" refid="external.build.dir" />
+            <property name="dist.dir" refid="external.dist.dir" />
+            <property name="gatk.classpath" refid="external.gatk.classpath" />
             <fileset dir="${external.dir}" includes="*/build.xml" erroronmissingdir="false" />
         </subant>
     </target>