From 9b84fa20bfbe6955c1309776b68b03040b29f505 Mon Sep 17 00:00:00 2001
From: David Roazen <droazen@broadinstitute.org>
Date: Wed, 15 Aug 2012 15:56:54 -0400
Subject: [PATCH] Fix an issue with the classpath for external builds in
 build.xml

Use "path" instead of "pathconvert" to construct the external.gatk.classpath.
This allows the path to evolve as the build progresses, instead of being
fixed early on to a value that (in some cases) could be incorrect.
---
 build.xml | 23 +++++++++--------------
 1 file changed, 9 insertions(+), 14 deletions(-)

diff --git a/build.xml b/build.xml
index 135b9dac7..2ca48c51b 100644
--- a/build.xml
+++ b/build.xml
@@ -70,13 +70,18 @@
     <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" />
     <property name="staging.dir" value="staging" />
     <property name="default.executable" value="none" />
 
-    <!-- Javadoc/Scaladoc directories -->
+    <!-- GATKDocs/Javadoc/Scaladoc directories -->
+    <property name="gatkdocs.dir" value="gatkdocs" />
     <property name="javadoc.dir" value="javadoc" />
     <property name="scaladoc.dir" value="scaladoc" />
 
@@ -96,8 +101,6 @@
     <property name="cofoja.jar" value="${lib.dir}/cofoja-${contracts.version}.jar"/>
     <property name="contract.dump.dir" value="dump" />
 
-    <property name="gatkdocs.dir" value="gatkdocs" />
-
     <!-- do we want to halt on failure of a unit test? default to yes (Bamboo uses 'no') -->
     <property name="halt" value="yes" />
 
@@ -208,19 +211,11 @@
         <include name="**/*.java" />
     </fileset>
 
-    <pathconvert property="external.build.dir">
-        <path path="${java.classes}"/>
-    </pathconvert>
-
-    <pathconvert property="external.dist.dir">
-        <path path="${dist.dir}" />
-    </pathconvert>
-
     <!-- GATK dependencies consist of 3rd party plugins plus compiled GATK classes -->
-    <pathconvert property="external.gatk.classpath">
+    <path id="external.gatk.classpath">
         <path path="${java.classes}"/>
         <path refid="external.dependencies" />
-    </pathconvert>
+    </path>
 
     <!-- the path for resources that need to go into the GATK jar;
          any additional resources should go into this set. -->
@@ -432,7 +427,7 @@
         <subant target="compile" genericantfile="build.xml">
             <property name="build.dir" value="${external.build.dir}" />
             <property name="dist.dir" value="${external.dist.dir}" />
-            <property name="gatk.classpath" value="${external.gatk.classpath}" />
+            <property name="gatk.classpath" refid="external.gatk.classpath" />
             <fileset dir="${external.dir}" includes="*/build.xml" erroronmissingdir="false" />
         </subant>
     </target>