diff --git a/core/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java b/core/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
index 1f98da4ff..403ab1643 100644
--- a/core/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
+++ b/core/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
@@ -15,7 +15,7 @@ import java.util.HashMap;
 
 public class GenomeAnalysisTK extends CommandLineProgram {
     // Usage and parameters
-    @Usage(programVersion="0.1") public String USAGE = "SAM Validator\n";
+    @Usage(programVersion="0.1") public String USAGE = "Genome Analysis Toolkit\n";
     @Option(shortName="I", doc="SAM or BAM file for validation") public File INPUT_FILE;
     @Option(shortName="M", doc="Maximum number of reads to process before exiting", optional=true) public String MAX_READS_ARG = "-1";
     @Option(shortName="S", doc="How strict should we be with validation", optional=true) public String STRICTNESS_ARG = "strict";
@@ -28,7 +28,10 @@ public class GenomeAnalysisTK extends CommandLineProgram {
     @Option(shortName="U", doc="If true, enables unsafe operations, nothing will be checked at runtime.  You better know what you are doing if you set this flag.", optional=false) public String UNSAFE = "false";
     @Option(shortName="SORT_ON_FLY", doc="If true, enables on fly sorting of reads file.", optional=false) public String ENABLED_SORT_ON_FLY = "false";
 
-    private WalkerManager walkerManager = new WalkerManager();
+    @Option(shortName="PLUGINS", doc="Directory where plugin class files live.", optional=true)
+    public String pluginPathName = null;
+
+    private WalkerManager walkerManager = null;
     
     private TraversalEngine engine = null;
     public boolean DEBUGGING = false;
@@ -39,6 +42,8 @@ public class GenomeAnalysisTK extends CommandLineProgram {
     }
 
     protected int doWork() {
+        walkerManager = new WalkerManager(pluginPathName);
+
         final boolean TEST_ROD = false;
         ReferenceOrderedData[] rods = null;
 
diff --git a/core/java/src/org/broadinstitute/sting/gatk/WalkerManager.java b/core/java/src/org/broadinstitute/sting/gatk/WalkerManager.java
index eed49c9c5..801e67a30 100755
--- a/core/java/src/org/broadinstitute/sting/gatk/WalkerManager.java
+++ b/core/java/src/org/broadinstitute/sting/gatk/WalkerManager.java
@@ -29,17 +29,25 @@ import org.broadinstitute.sting.gatk.walkers.Walker;
  * To change this template use File | Settings | File Templates.
  */
 public class WalkerManager {
+    
     private Map<String,Walker> walkers = null;
 
-    public WalkerManager() {
+    public WalkerManager( String pluginDirectory ) {
         try {
             final File jarFile = getThisJarFile();
 
+            if(pluginDirectory == null)
+                pluginDirectory = jarFile.getParent() + File.separator + "walkers";
+
+            System.out.println("plugin directory: " + pluginDirectory);
+
             List<Class> walkerClasses = new ArrayList<Class>();
 
-            walkerClasses.addAll( loadClassesFromJar( jarFile, getPackagePrefix(Walker.class) ) );
+            // Load all classes that live in this jar.
+            walkerClasses.addAll( loadClassesFromJar( jarFile ) );
 
-            File extensionPath = new File( jarFile.getParent() + File.separator + "walkers" );
+            // Load all classes that live in the extension path.
+            File extensionPath = new File( pluginDirectory );
             if(extensionPath.exists())
                 walkerClasses.addAll( loadClassesFromPath( extensionPath ) );
 
@@ -102,10 +110,9 @@ public class WalkerManager {
      * Loads concrete classes from a jar which are both in the same package or 'sub-package' of baseClass,
      * and which extend from baseClass.
      * @param jarFile The jar file to search.
-     * @param packagePrefix Filter out classes in the jar that don't start with this package.
      * @return A list of classes derived from baseClass.
      */
-    private List<Class> loadClassesFromJar(final File jarFile, String packagePrefix)
+    private List<Class> loadClassesFromJar(final File jarFile)
             throws IOException {
         List<Class> subclasses = new ArrayList<Class>();
 
@@ -116,7 +123,7 @@ public class WalkerManager {
 
             while(jarEntry != null) {
                 String jarEntryName = jarEntry.getName();
-                if(jarEntryName.startsWith(packagePrefix) && jarEntryName.endsWith(".class"))
+                if(jarEntryName.endsWith(".class"))
                 {
                     String className = jarEntryName.substring(0,jarEntryName.lastIndexOf(".class")).replace('/','.');
                     subclasses.add( Class.forName(className) );
@@ -135,15 +142,6 @@ public class WalkerManager {
         return subclasses;
     }
 
-    /**
-     * Get the package prefix for a class, in directory format.
-     * @param clazz The class.
-     * @return Package prefix, in directory format.
-     */
-    private String getPackagePrefix(Class clazz) {
-        return clazz.getPackage().getName().replace('.','/');
-    }
-
     /**
      * Load loose classes from the specified directory.
      * @param path source path from which to load classes.