picard-tools (1.27-1) 01-build.xml

Description: Modifies the upstream build system.
 This patch changes the path to the javac compiler, enables the use
 of the system's testng library, and adds a new target for preparing
 the sam and picard jar files and installing the extra R scripts
 from src/scripts/net/sf/picard/analysis/.
Origin: vendor
Forwarded: no
--- picard-tools.orig/build.xml
+++ picard-tools/build.xml
@@ -23,7 +23,7 @@
   ~ THE SOFTWARE.
   -->
 
-<project name="picard-public" basedir="." default="all">
+<project name="picard-public" basedir="." default="jar">
 
     <property name="src" value="src/java"/>
     <property name="src.scripts" value="src/scripts"/>
@@ -74,6 +74,7 @@
             <fileset dir="${lib}">
                 <include name="**/*.jar"/>
             </fileset>
+            <pathelement path="/usr/share/java/testng.jar"/>
         </path>
         <path  id="metrics.classpath">
             <pathelement path="${classpath}"/>
@@ -108,7 +109,7 @@
                sourcepath="" srcdir="${src}"
                includes ="net/sf/samtools/**/*.*"
                excludes = "net/sf/picard/**/*.*"
-               executable="${JAVA_HOME_1_5}/bin/javac"
+               executable="javac"
                compiler="javac1.5" fork="true">
             <!--<compilerarg value="-Xlint:all"/>-->
             <!--<compilerarg value="-Xlint:unchecked"/>-->
@@ -137,7 +138,7 @@
                optimize="${javac.opt}"
                debug="${javac.debug}"
                includes ="net/sf/samtools/**/*.*"
-               executable="${JAVA_HOME_1_5}/bin/javac"
+               executable="javac"
                compiler="javac1.5" fork="true"> <!-- Force SAM-JDK to be built with 1.5 -->
             <!--<compilerarg value="-Xlint:unchecked"/>-->
             <src path="${src.test}"/>
@@ -221,9 +222,12 @@
         <mkdir dir="${dist}"/>
         <jar destfile="${dist}/picard-${picard-version}.jar" compress="no">
             <fileset dir="${classes}" includes ="net/sf/picard/**/*.*"/>
+            <fileset dir="${src.scripts}" includes="**/*.R"/>
         </jar>
     </target>
 
+    <target name="jar" depends="sam-jar, picard-jar" />
+
     <target name="javadoc" depends="init" description="Generates the project javadoc.">
         <javadoc
                 sourcepath="${src}"