diff --git a/fullstack/pregelix/pregelix-example/pom.xml b/fullstack/pregelix/pregelix-example/pom.xml
index beefee2..20c45ec 100644
--- a/fullstack/pregelix/pregelix-example/pom.xml
+++ b/fullstack/pregelix/pregelix-example/pom.xml
@@ -24,6 +24,7 @@
 			</plugin>
 			<plugin>
 				<artifactId>maven-assembly-plugin</artifactId>
+                <version>2.2-beta-5</version>
 				<configuration>
 					<descriptorRefs>
 						<descriptorRef>jar-with-dependencies</descriptorRef>
@@ -42,7 +43,7 @@
 			<plugin>
 				<groupId>org.codehaus.mojo</groupId>
 				<artifactId>appassembler-maven-plugin</artifactId>
-				<version>1.3</version>
+                <version>1.3</version>
 				<executions>
 					<execution>
 						<configuration>
@@ -79,7 +80,7 @@
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-clean-plugin</artifactId>
-				<version>2.5</version>
+				<version>2.4.1</version>
 				<configuration>
 					<filesets>
 						<fileset>
diff --git a/fullstack/pregelix/pregelix-example/src/test/java/edu/uci/ics/pregelix/example/dataload/DataLoadTest.java b/fullstack/pregelix/pregelix-example/src/test/java/edu/uci/ics/pregelix/example/dataload/DataLoadTest.java
index 321b5b2..da6d564 100644
--- a/fullstack/pregelix/pregelix-example/src/test/java/edu/uci/ics/pregelix/example/dataload/DataLoadTest.java
+++ b/fullstack/pregelix/pregelix-example/src/test/java/edu/uci/ics/pregelix/example/dataload/DataLoadTest.java
@@ -76,8 +76,7 @@
         ClusterConfig.setStorePath(PATH_TO_CLUSTER_STORE);
         ClusterConfig.setClusterPropertiesPath(PATH_TO_CLUSTER_PROPERTIES);
         cleanupStores();
-        PregelixHyracksIntegrationUtil.init("src/test/resources/topology.xml");
-        PregelixHyracksIntegrationUtil.createApp(HYRACKS_APP_NAME);
+        PregelixHyracksIntegrationUtil.init();
         LOGGER.info("Hyracks mini-cluster started");
         startHDFS();
         FileUtils.forceMkdir(new File(EXPECT_RESULT_DIR));
@@ -112,7 +111,6 @@
     }
 
     public void tearDown() throws Exception {
-        PregelixHyracksIntegrationUtil.destroyApp(HYRACKS_APP_NAME);
         PregelixHyracksIntegrationUtil.deinit();
         LOGGER.info("Hyracks mini-cluster shut down");
         cleanupHDFS();
diff --git a/fullstack/pregelix/pregelix-example/src/test/java/edu/uci/ics/pregelix/example/jobrun/RunJobTestSuite.java b/fullstack/pregelix/pregelix-example/src/test/java/edu/uci/ics/pregelix/example/jobrun/RunJobTestSuite.java
index fa98ebd..4bf83e6 100644
--- a/fullstack/pregelix/pregelix-example/src/test/java/edu/uci/ics/pregelix/example/jobrun/RunJobTestSuite.java
+++ b/fullstack/pregelix/pregelix-example/src/test/java/edu/uci/ics/pregelix/example/jobrun/RunJobTestSuite.java
@@ -41,176 +41,166 @@
 
 @SuppressWarnings("deprecation")
 public class RunJobTestSuite extends TestSuite {
-	private static final Logger LOGGER = Logger.getLogger(RunJobTestSuite.class
-			.getName());
+    private static final Logger LOGGER = Logger.getLogger(RunJobTestSuite.class.getName());
 
-	private static final String ACTUAL_RESULT_DIR = "actual";
-	private static final String EXPECTED_RESULT_DIR = "src/test/resources/expected";
-	private static final String PATH_TO_HADOOP_CONF = "src/test/resources/hadoop/conf";
-	private static final String PATH_TO_CLUSTER_STORE = "src/test/resources/cluster/stores.properties";
-	private static final String PATH_TO_CLUSTER_PROPERTIES = "src/test/resources/cluster/cluster.properties";
-	private static final String PATH_TO_JOBS = "src/test/resources/jobs/";
-	private static final String PATH_TO_IGNORE = "src/test/resources/ignore.txt";
-	private static final String PATH_TO_ONLY = "src/test/resources/only.txt";
-	private static final String FILE_EXTENSION_OF_RESULTS = "result";
+    private static final String ACTUAL_RESULT_DIR = "actual";
+    private static final String EXPECTED_RESULT_DIR = "src/test/resources/expected";
+    private static final String PATH_TO_HADOOP_CONF = "src/test/resources/hadoop/conf";
+    private static final String PATH_TO_CLUSTER_STORE = "src/test/resources/cluster/stores.properties";
+    private static final String PATH_TO_CLUSTER_PROPERTIES = "src/test/resources/cluster/cluster.properties";
+    private static final String PATH_TO_JOBS = "src/test/resources/jobs/";
+    private static final String PATH_TO_IGNORE = "src/test/resources/ignore.txt";
+    private static final String PATH_TO_ONLY = "src/test/resources/only.txt";
+    private static final String FILE_EXTENSION_OF_RESULTS = "result";
 
-	private static final String DATA_PATH = "data/webmap/webmap_link.txt";
-	private static final String HDFS_PATH = "/webmap/";
+    private static final String DATA_PATH = "data/webmap/webmap_link.txt";
+    private static final String HDFS_PATH = "/webmap/";
 
-	private static final String DATA_PATH2 = "data/webmapcomplex/webmap_link.txt";
-	private static final String HDFS_PATH2 = "/webmapcomplex/";
+    private static final String DATA_PATH2 = "data/webmapcomplex/webmap_link.txt";
+    private static final String HDFS_PATH2 = "/webmapcomplex/";
 
-	private static final String DATA_PATH3 = "data/clique/clique.txt";
-	private static final String HDFS_PATH3 = "/clique/";
+    private static final String DATA_PATH3 = "data/clique/clique.txt";
+    private static final String HDFS_PATH3 = "/clique/";
 
-	private static final String HYRACKS_APP_NAME = "pregelix";
-	private static final String HADOOP_CONF_PATH = ACTUAL_RESULT_DIR
-			+ File.separator + "conf.xml";
-	private MiniDFSCluster dfsCluster;
+    private static final String HYRACKS_APP_NAME = "pregelix";
+    private static final String HADOOP_CONF_PATH = ACTUAL_RESULT_DIR + File.separator + "conf.xml";
+    private MiniDFSCluster dfsCluster;
 
-	private JobConf conf = new JobConf();
-	private int numberOfNC = 2;
+    private JobConf conf = new JobConf();
+    private int numberOfNC = 2;
 
-	public void setUp() throws Exception {
-		ClusterConfig.setStorePath(PATH_TO_CLUSTER_STORE);
-		ClusterConfig.setClusterPropertiesPath(PATH_TO_CLUSTER_PROPERTIES);
-		cleanupStores();
-		PregelixHyracksIntegrationUtil.init("src/test/resources/topology.xml");
-		PregelixHyracksIntegrationUtil.createApp(HYRACKS_APP_NAME);
-		LOGGER.info("Hyracks mini-cluster started");
-		FileUtils.forceMkdir(new File(ACTUAL_RESULT_DIR));
-		FileUtils.cleanDirectory(new File(ACTUAL_RESULT_DIR));
-		startHDFS();
-	}
+    public void setUp() throws Exception {
+        ClusterConfig.setStorePath(PATH_TO_CLUSTER_STORE);
+        ClusterConfig.setClusterPropertiesPath(PATH_TO_CLUSTER_PROPERTIES);
+        cleanupStores();
+        PregelixHyracksIntegrationUtil.init();
+        LOGGER.info("Hyracks mini-cluster started");
+        FileUtils.forceMkdir(new File(ACTUAL_RESULT_DIR));
+        FileUtils.cleanDirectory(new File(ACTUAL_RESULT_DIR));
+        startHDFS();
+    }
 
-	private void cleanupStores() throws IOException {
-		FileUtils.forceMkdir(new File("teststore"));
-		FileUtils.forceMkdir(new File("build"));
-		FileUtils.cleanDirectory(new File("teststore"));
-		FileUtils.cleanDirectory(new File("build"));
-	}
+    private void cleanupStores() throws IOException {
+        FileUtils.forceMkdir(new File("teststore"));
+        FileUtils.forceMkdir(new File("build"));
+        FileUtils.cleanDirectory(new File("teststore"));
+        FileUtils.cleanDirectory(new File("build"));
+    }
 
-	private void startHDFS() throws IOException {
-		conf.addResource(new Path(PATH_TO_HADOOP_CONF + "/core-site.xml"));
-		conf.addResource(new Path(PATH_TO_HADOOP_CONF + "/mapred-site.xml"));
-		conf.addResource(new Path(PATH_TO_HADOOP_CONF + "/hdfs-site.xml"));
-		FileSystem lfs = FileSystem.getLocal(new Configuration());
-		lfs.delete(new Path("build"), true);
-		System.setProperty("hadoop.log.dir", "logs");
-		dfsCluster = new MiniDFSCluster(conf, numberOfNC, true, null);
-		FileSystem dfs = FileSystem.get(conf);
-		Path src = new Path(DATA_PATH);
-		Path dest = new Path(HDFS_PATH);
-		dfs.mkdirs(dest);
-		dfs.copyFromLocalFile(src, dest);
+    private void startHDFS() throws IOException {
+        conf.addResource(new Path(PATH_TO_HADOOP_CONF + "/core-site.xml"));
+        conf.addResource(new Path(PATH_TO_HADOOP_CONF + "/mapred-site.xml"));
+        conf.addResource(new Path(PATH_TO_HADOOP_CONF + "/hdfs-site.xml"));
+        FileSystem lfs = FileSystem.getLocal(new Configuration());
+        lfs.delete(new Path("build"), true);
+        System.setProperty("hadoop.log.dir", "logs");
+        dfsCluster = new MiniDFSCluster(conf, numberOfNC, true, null);
+        FileSystem dfs = FileSystem.get(conf);
+        Path src = new Path(DATA_PATH);
+        Path dest = new Path(HDFS_PATH);
+        dfs.mkdirs(dest);
+        dfs.copyFromLocalFile(src, dest);
 
-		src = new Path(DATA_PATH2);
-		dest = new Path(HDFS_PATH2);
-		dfs.mkdirs(dest);
-		dfs.copyFromLocalFile(src, dest);
+        src = new Path(DATA_PATH2);
+        dest = new Path(HDFS_PATH2);
+        dfs.mkdirs(dest);
+        dfs.copyFromLocalFile(src, dest);
 
-		src = new Path(DATA_PATH3);
-		dest = new Path(HDFS_PATH3);
-		dfs.mkdirs(dest);
-		dfs.copyFromLocalFile(src, dest);
+        src = new Path(DATA_PATH3);
+        dest = new Path(HDFS_PATH3);
+        dfs.mkdirs(dest);
+        dfs.copyFromLocalFile(src, dest);
 
-		DataOutputStream confOutput = new DataOutputStream(
-				new FileOutputStream(new File(HADOOP_CONF_PATH)));
-		conf.writeXml(confOutput);
-		confOutput.flush();
-		confOutput.close();
-	}
+        DataOutputStream confOutput = new DataOutputStream(new FileOutputStream(new File(HADOOP_CONF_PATH)));
+        conf.writeXml(confOutput);
+        confOutput.flush();
+        confOutput.close();
+    }
 
-	/**
-	 * cleanup hdfs cluster
-	 */
-	private void cleanupHDFS() throws Exception {
-		dfsCluster.shutdown();
-	}
+    /**
+     * cleanup hdfs cluster
+     */
+    private void cleanupHDFS() throws Exception {
+        dfsCluster.shutdown();
+    }
 
-	public void tearDown() throws Exception {
-		PregelixHyracksIntegrationUtil.destroyApp(HYRACKS_APP_NAME);
-		PregelixHyracksIntegrationUtil.deinit();
-		LOGGER.info("Hyracks mini-cluster shut down");
-		cleanupHDFS();
-	}
+    public void tearDown() throws Exception {
+        PregelixHyracksIntegrationUtil.deinit();
+        LOGGER.info("Hyracks mini-cluster shut down");
+        cleanupHDFS();
+    }
 
-	public static Test suite() throws Exception {
-		List<String> ignores = getFileList(PATH_TO_IGNORE);
-		List<String> onlys = getFileList(PATH_TO_ONLY);
-		File testData = new File(PATH_TO_JOBS);
-		File[] queries = testData.listFiles();
-		RunJobTestSuite testSuite = new RunJobTestSuite();
-		testSuite.setUp();
-		boolean onlyEnabled = false;
+    public static Test suite() throws Exception {
+        List<String> ignores = getFileList(PATH_TO_IGNORE);
+        List<String> onlys = getFileList(PATH_TO_ONLY);
+        File testData = new File(PATH_TO_JOBS);
+        File[] queries = testData.listFiles();
+        RunJobTestSuite testSuite = new RunJobTestSuite();
+        testSuite.setUp();
+        boolean onlyEnabled = false;
 
-		if (onlys.size() > 0) {
-			onlyEnabled = true;
-		}
-		for (File qFile : queries) {
-			if (isInList(ignores, qFile.getName()))
-				continue;
+        if (onlys.size() > 0) {
+            onlyEnabled = true;
+        }
+        for (File qFile : queries) {
+            if (isInList(ignores, qFile.getName()))
+                continue;
 
-			if (qFile.isFile()) {
-				if (onlyEnabled && !isInList(onlys, qFile.getName())) {
-					continue;
-				} else {
-					String resultFileName = ACTUAL_RESULT_DIR + File.separator
-							+ jobExtToResExt(qFile.getName());
-					String expectedFileName = EXPECTED_RESULT_DIR
-							+ File.separator + jobExtToResExt(qFile.getName());
-					testSuite.addTest(new RunJobTestCase(HADOOP_CONF_PATH,
-							qFile.getName(),
-							qFile.getAbsolutePath().toString(), resultFileName,
-							expectedFileName));
-				}
-			}
-		}
-		return testSuite;
-	}
+            if (qFile.isFile()) {
+                if (onlyEnabled && !isInList(onlys, qFile.getName())) {
+                    continue;
+                } else {
+                    String resultFileName = ACTUAL_RESULT_DIR + File.separator + jobExtToResExt(qFile.getName());
+                    String expectedFileName = EXPECTED_RESULT_DIR + File.separator + jobExtToResExt(qFile.getName());
+                    testSuite.addTest(new RunJobTestCase(HADOOP_CONF_PATH, qFile.getName(), qFile.getAbsolutePath()
+                            .toString(), resultFileName, expectedFileName));
+                }
+            }
+        }
+        return testSuite;
+    }
 
-	/**
-	 * Runs the tests and collects their result in a TestResult.
-	 */
-	@Override
-	public void run(TestResult result) {
-		try {
-			int testCount = countTestCases();
-			for (int i = 0; i < testCount; i++) {
-				// cleanupStores();
-				Test each = this.testAt(i);
-				if (result.shouldStop())
-					break;
-				runTest(each, result);
-			}
-			tearDown();
-		} catch (Exception e) {
-			throw new IllegalStateException(e);
-		}
-	}
+    /**
+     * Runs the tests and collects their result in a TestResult.
+     */
+    @Override
+    public void run(TestResult result) {
+        try {
+            int testCount = countTestCases();
+            for (int i = 0; i < testCount; i++) {
+                // cleanupStores();
+                Test each = this.testAt(i);
+                if (result.shouldStop())
+                    break;
+                runTest(each, result);
+            }
+            tearDown();
+        } catch (Exception e) {
+            throw new IllegalStateException(e);
+        }
+    }
 
-	protected static List<String> getFileList(String ignorePath)
-			throws FileNotFoundException, IOException {
-		BufferedReader reader = new BufferedReader(new FileReader(ignorePath));
-		String s = null;
-		List<String> ignores = new ArrayList<String>();
-		while ((s = reader.readLine()) != null) {
-			ignores.add(s);
-		}
-		reader.close();
-		return ignores;
-	}
+    protected static List<String> getFileList(String ignorePath) throws FileNotFoundException, IOException {
+        BufferedReader reader = new BufferedReader(new FileReader(ignorePath));
+        String s = null;
+        List<String> ignores = new ArrayList<String>();
+        while ((s = reader.readLine()) != null) {
+            ignores.add(s);
+        }
+        reader.close();
+        return ignores;
+    }
 
-	private static String jobExtToResExt(String fname) {
-		int dot = fname.lastIndexOf('.');
-		return fname.substring(0, dot + 1) + FILE_EXTENSION_OF_RESULTS;
-	}
+    private static String jobExtToResExt(String fname) {
+        int dot = fname.lastIndexOf('.');
+        return fname.substring(0, dot + 1) + FILE_EXTENSION_OF_RESULTS;
+    }
 
-	private static boolean isInList(List<String> onlys, String name) {
-		for (String only : onlys)
-			if (name.indexOf(only) >= 0)
-				return true;
-		return false;
-	}
+    private static boolean isInList(List<String> onlys, String name) {
+        for (String only : onlys)
+            if (name.indexOf(only) >= 0)
+                return true;
+        return false;
+    }
 
 }