Updated google reflections due to stale slf4j version conflicting with other projects also trying to use Queue as a component.

Added targets to build.xml to effectively 'mvn install' packaged GATK/Queue from ant.
TODO: Versions during 'mvn install' are hardcoded at 0.0.1 until a better versioning scheme that works with maven dependencies has been identified.

build.xml

@@ -22,7 +22,9 @@
   ~ OTHER DEALINGS IN THE SOFTWARE.
   -->
 
-<project name="Sting" default="dist" basedir="." xmlns:ivy="antlib:org.apache.ivy.ant">
+<project name="Sting" default="dist" basedir="."
+         xmlns:artifact="antlib:org.apache.maven.artifact.ant"
+         xmlns:ivy="antlib:org.apache.ivy.ant">
     <description>Compile and distribute the Sting toolkit</description>
 
     <!-- ******************************************************************************** -->
@@ -250,11 +252,14 @@
         <property name="ivy.jar.file" value="ivy-${ivy.install.version}.jar"/>
         <property name="ivy.settings.dir" value="settings"/>
         <property file="${ivy.settings.dir}/ivysettings.properties"/>
+        <property name="maven-ant-tasks.install.version" value="2.1.3"/>
+        <property name="maven-ant-tasks.jar.file" value="maven-ant-tasks-${maven-ant-tasks.install.version}.jar"/>
 
         <mkdir dir="${lib.dir}"/>
         <mkdir dir="${ivy.jar.dir}"/>
 
-        <!-- Comment out the following two lines to build the GATK without a network connection, assuming you have all of the libraries cached already -->
+        <!-- Comment out the following lines to build the GATK without a network connection, assuming you have all of the libraries cached already -->
+
         <get src="http://repo1.maven.org/maven2/org/apache/ivy/ivy/${ivy.install.version}/${ivy.jar.file}"
              dest="${ivy.jar.dir}/${ivy.jar.file}"
              usetimestamp="true"/>
@@ -262,6 +267,15 @@
                  uri="antlib:org.apache.ivy.ant"
                  classpath="${ivy.jar.dir}/${ivy.jar.file}"/>
 
+        <get src="http://repo1.maven.org/maven2/org/apache/maven/maven-ant-tasks/${maven-ant-tasks.install.version}/${maven-ant-tasks.jar.file}"
+             dest="${ivy.jar.dir}/${maven-ant-tasks.jar.file}"
+             usetimestamp="true"/>
+        <taskdef resource="org/apache/maven/artifact/ant/antlib.xml"
+                 uri="antlib:antlib:org.apache.maven.artifact.ant"
+                 classpath="${ivy.jar.dir}/${maven-ant-tasks.jar.file}"/>
+
+        <!-- End network lines -->
+
         <ivy:settings file="${ivy.settings.dir}/ivysettings.xml"/>
         <property name="init.resolve.done" value="true"/>
     </target>
@@ -295,7 +309,7 @@
 
     <target name="git.rev-parse" depends="git.describe" unless="git.describe.succeeded">
       <exec executable="git" outputproperty="git.rev-parse.output" resultproperty="git.rev-parse.exit.value" failonerror="false">
-        <arg line="rev-parse HEAD" />
+        <arg line="rev-parse --short HEAD" />
       </exec>
       <condition property="git.rev-parse.succeeded">
         <equals arg1="${git.rev-parse.exit.value}" arg2="0" />
@@ -942,6 +956,28 @@
       </ant>
     </target>
 
+    <!-- Maven install a package consisting of all supporting files. Don't call this target directly. Call one of the specific packaging targets below -->
+    <target name="mvninstall" depends="package" description="maven install a package into .m2/repository">
+        <property name="mvn.build.version" value="0.0.1" />
+        <!--
+        We should use the build version or better yet a git tag version, but tags are currently missing. Alternatively how do we then depend on the LATEST?
+        <property name="mvn.build.version" value="${build.version}" />
+        -->
+        <artifact:pom id="${executable}.pom" groupId="org.broadinstitute.sting" artifactId="${executable}" version="${mvn.build.version}" name="${executable}" />
+        <artifact:writepom pomRefId="${executable}.pom" file="${package.output.dir}/${executable}-${build.version}/${executable}.pom.xml"/>
+        <artifact:install file="${package.output.dir}/${executable}-${build.version}/${executable}.jar">
+            <artifact:pom file="${package.output.dir}/${executable}-${build.version}/${executable}.pom.xml" />
+        </artifact:install>
+    </target>
+
+    <!-- Maven install specific versions of the GATK/Queue. ALWAYS do an ant clean before invoking these! -->
+    <target name="mvninstall.gatk.full" depends="package.gatk.full,mvninstall" />
+
+    <target name="mvninstall.gatk.lite" depends="package.gatk.lite,mvninstall" />
+
+    <target name="mvninstall.queue.full" depends="package.queue.full,mvninstall" />
+
+    <target name="mvninstall.queue.lite" depends="package.queue.lite,mvninstall" />
 
     <!-- ******************************************************************************** -->
     <!-- Clean                                                                            -->

ivy.xml

@@ -46,7 +46,8 @@
         <dependency org="org.apache.bcel" name="bcel" rev="5.2"/>
 
         <!-- Dependencies for reflections mvn repository -->
-        <dependency org="org.reflections" name="reflections" rev="0.9.5-RC2"/>
+        <dependency org="org.reflections" name="reflections" rev="0.9.8"/>
+        <dependency org="org.slf4j" name="slf4j-log4j12" rev="1.6.1"/>
 
         <!-- Matrix package from math.nist.gov -->
         <dependency org="gov.nist" name="Jama" rev="1.0.2"/>

public/java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java

@@ -32,7 +32,6 @@ import org.reflections.util.ClasspathHelper;
 
 import java.io.File;
 import java.io.IOException;
-import java.lang.annotation.Annotation;
 import java.lang.reflect.*;
 import java.net.URL;
 import java.util.*;
@@ -198,7 +197,7 @@ public class JVMUtils {
      * @return the list of class path urls.
      */
     public static Set<URL> getClasspathURLs() {
-        return ClasspathHelper.getUrlsForManifestsCurrentClasspath();
+        return ClasspathHelper.forManifest();
     }
 
     /**
@@ -240,8 +239,8 @@ public class JVMUtils {
     /**
      * Returns a comma-separated list of the names of the interfaces implemented by this class
      *
-     * @param covClass
-     * @return
+     * @param covClass class
+     * @return names of interfaces
      */
     public static String classInterfaces(final Class covClass) {
         final List<String> interfaces = new ArrayList<String>();

public/java/src/org/broadinstitute/sting/utils/classloader/PluginManager.java

@@ -25,8 +25,6 @@
 
 package org.broadinstitute.sting.utils.classloader;
 
-import ch.qos.logback.classic.Level;
-import ch.qos.logback.classic.Logger;
 import org.broadinstitute.sting.gatk.WalkerManager;
 import org.broadinstitute.sting.gatk.filters.FilterManager;
 import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
@@ -35,7 +33,6 @@ import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.reflections.Reflections;
 import org.reflections.scanners.SubTypesScanner;
 import org.reflections.util.ConfigurationBuilder;
-import org.slf4j.LoggerFactory;
 
 import java.io.File;
 import java.lang.reflect.Constructor;
@@ -57,9 +54,8 @@ public class PluginManager<PluginType> {
     private static final Reflections defaultReflections;
 
     static {
-        // turn off logging in the reflections library - they talk too much (to the wrong logger factory as well, logback)
-        Logger logger = (ch.qos.logback.classic.Logger) LoggerFactory.getLogger(Reflections.class);
-        logger.setLevel(Level.OFF);
+        // turn off logging in the reflections library - they talk too much
+        Reflections.log = null;
 
         Set<URL> classPathUrls = new LinkedHashSet<URL>();
 
@@ -179,9 +175,9 @@ public class PluginManager<PluginType> {
     /**
      * Sorts, in place, the list of plugins according to getName() on each element
      *
-     * @param unsortedPlugins
+     * @param unsortedPlugins unsorted plugins
      */
-    private final void sortPlugins(final List<Class<? extends PluginType>> unsortedPlugins) {
+    private void sortPlugins(final List<Class<? extends PluginType>> unsortedPlugins) {
         Collections.sort(unsortedPlugins, new ComparePluginsByName());
     }
 
@@ -235,7 +231,7 @@ public class PluginManager<PluginType> {
      * @param plugin Name of the plugin for which to search.
      * @return True if the plugin exists, false otherwise.
      */
-    public boolean exists(Class<?> plugin) {
+    public boolean exists(Class<? extends PluginType> plugin) {
         return pluginsByName.containsValue(plugin);
     }
 

settings/ivysettings.xml

@@ -7,7 +7,6 @@
 	<artifact pattern="${repository.dir}/[organisation]/[artifact]-[revision].[ext]" />
 	<ivy pattern="${repository.dir}/[organisation]/[module]-[revision].xml" />
       </filesystem>
-      <ibiblio name="reflections-repo" m2compatible="true" root="http://reflections.googlecode.com/svn/repo" />
       <ibiblio name="maven" root="http://repo1.maven.org/maven2" m2compatible="true" />
     </chain>
   </resolvers>