diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/minicluster/GenomixMiniCluster.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/minicluster/GenomixMiniCluster.java
index 09f7db9..abaac30 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/minicluster/GenomixMiniCluster.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/minicluster/GenomixMiniCluster.java
@@ -1,32 +1,91 @@
 package edu.uci.ics.genomix.minicluster;
 
-import java.io.File;
 import java.io.IOException;
 import java.io.PrintWriter;
 import java.nio.file.FileSystems;
 import java.nio.file.Files;
-import java.nio.file.attribute.FileAttribute;
 import java.nio.file.Path;
 
+import org.apache.commons.io.FileUtils;
 import org.apache.hadoop.hdfs.MiniDFSCluster;
+import org.apache.wicket.util.file.File;
 
 import edu.uci.ics.pregelix.core.jobgen.clusterconfig.ClusterConfig;
-import edu.uci.ics.pregelix.core.util.PregelixHyracksIntegrationUtil;
+import edu.uci.ics.pregelix.runtime.bootstrap.NCApplicationEntryPoint;
 import edu.uci.ics.genomix.config.GenomixJobConf;
+import edu.uci.ics.hyracks.control.cc.ClusterControllerService;
+import edu.uci.ics.hyracks.control.common.controllers.CCConfig;
+import edu.uci.ics.hyracks.control.common.controllers.NCConfig;
+import edu.uci.ics.hyracks.control.nc.NodeControllerService;
 
-@SuppressWarnings("deprecation")
 public class GenomixMiniCluster {
-    private MiniDFSCluster dfsCluster;
-    private Path clusterProperties;
-    private Path clusterStores;
-    private Path clusterWorkDir;
-    private Path clusterStoresDir;
+    
+    public static final String NC1_ID = "nc1";
+    public static final int TEST_HYRACKS_CC_PORT = 1099;
+    public static final int TEST_HYRACKS_CC_CLIENT_PORT = 2099;
+    public static final String CC_HOST = "localhost";
 
-    private void makeLocalClusterConfig() throws IOException {
+    private static ClusterControllerService cc;
+    private static NodeControllerService nc1;
+    private static MiniDFSCluster dfsCluster;
+    private static Path clusterProperties;
+    private static Path clusterStores;
+    private static Path clusterWorkDir;
+    private static Path clusterStoresDir;
+    
+    public static void init(GenomixJobConf conf) throws Exception {
+        makeLocalClusterConfig();
+        ClusterConfig.setClusterPropertiesPath(clusterProperties.toAbsolutePath().toString());
+        ClusterConfig.setStorePath(clusterStores.toAbsolutePath().toString());
+//        dfsCluster = new MiniDFSCluster(conf, Integer.parseInt(conf.get(GenomixJobConf.CPARTITION_PER_MACHINE)), true, null);
+        
+        // cluster controller
+        CCConfig ccConfig = new CCConfig();
+        ccConfig.clientNetIpAddress = CC_HOST;
+        ccConfig.clusterNetIpAddress = CC_HOST;
+        ccConfig.clusterNetPort = TEST_HYRACKS_CC_PORT;
+        ccConfig.clientNetPort = TEST_HYRACKS_CC_CLIENT_PORT;
+        ccConfig.defaultMaxJobAttempts = 0;
+        ccConfig.jobHistorySize = 1;
+        ccConfig.profileDumpPeriod = -1;
+        cc = new ClusterControllerService(ccConfig);
+        cc.start();
+
+        // one node controller
+        NCConfig ncConfig1 = new NCConfig();
+        ncConfig1.ccHost = "localhost";
+        ncConfig1.clusterNetIPAddress = "localhost";
+        ncConfig1.ccPort = TEST_HYRACKS_CC_PORT;
+        ncConfig1.dataIPAddress = "127.0.0.1";
+        ncConfig1.datasetIPAddress = "127.0.0.1";
+        ncConfig1.nodeId = NC1_ID;
+        ncConfig1.ioDevices = clusterWorkDir.toString() + File.separator + "tmp" + File.separator + "t3";
+        ncConfig1.appNCMainClass = NCApplicationEntryPoint.class.getName();
+        nc1 = new NodeControllerService(ncConfig1);
+        nc1.start();
+    }
+
+    public static void deinit() throws Exception {
+        nc1.stop();
+        cc.stop();
+//        dfsCluster.shutdown();
+        FileUtils.deleteQuietly(new File("build"));
+        FileUtils.deleteQuietly(clusterProperties.toFile());
+        FileUtils.deleteQuietly(clusterStores.toFile());
+        FileUtils.deleteQuietly(clusterWorkDir.toFile());
+        FileUtils.deleteQuietly(clusterStoresDir.toFile());
+    }
+
+    /**
+     * create the necessary .properties and directories for a minicluster instance 
+     */
+    private static void makeLocalClusterConfig() throws IOException {
         clusterProperties = Files.createTempFile(FileSystems.getDefault().getPath("."), "tmp.cluster", ".properties");
         clusterWorkDir = Files.createTempDirectory(FileSystems.getDefault().getPath("."), "tmp.clusterWorkDir");
         PrintWriter writer = new PrintWriter(clusterProperties.toString(), "US-ASCII");
-        writer.println(String.format("WORKPATH=\"%s\"", clusterWorkDir.toAbsolutePath().toString()));
+        writer.println("CC_CLIENTPORT=" + TEST_HYRACKS_CC_CLIENT_PORT);
+        writer.println("CC_CLUSTERPORT=" + TEST_HYRACKS_CC_PORT);
+        writer.println(String.format("WORKPATH=%s", clusterWorkDir.toAbsolutePath().toString()));
         writer.println("CCTMP_DIR=${WORKPATH}/tmp/t1");
         writer.println("NCTMP_DIR=${WORKPATH}/tmp/t2");
         writer.println("CCLOGS_DIR=$CCTMP_DIR/logs");
@@ -42,21 +101,7 @@
         clusterStoresDir = Files.createTempDirectory(FileSystems.getDefault().getPath("."), "tmp.clusterStores");
         clusterStores = Files.createTempFile(FileSystems.getDefault().getPath("."), "tmp.stores", ".properties");
         writer = new PrintWriter(clusterStores.toString(), "US-ASCII");
-        writer.println(String.format("store=\"%s\"", clusterStoresDir.toAbsolutePath().toString()));
+        writer.println(String.format("store=%s", clusterStoresDir.toString()));
         writer.close();
     }
-
-    public void setUp(GenomixJobConf conf, String clusterStore, String clusterProperties) throws Exception {
-        makeLocalClusterConfig();
-        ClusterConfig.setClusterPropertiesPath(clusterPropertiesDir.toAbsolutePath().toString() + File.separator + "cluster.properties");
-        ClusterConfig.setStorePath(clusterPropertiesDir.toAbsolutePath().toString() + File.separator + "stores.properties");
-        PregelixHyracksIntegrationUtil.init();
-        dfsCluster = new MiniDFSCluster(conf, Integer.parseInt(conf.get(GenomixJobConf.CPARTITION_PER_MACHINE)), true,
-                null);
-    }
-
-    public void tearDown() throws Exception {
-        PregelixHyracksIntegrationUtil.deinit();
-        dfsCluster.shutdown();
-    }
 }
diff --git a/genomix/genomix-driver/data/AddBridge/SimpleTest/text.txt b/genomix/genomix-driver/data/AddBridge/SimpleTest/text.txt
deleted file mode 100755
index 01c49e5..0000000
--- a/genomix/genomix-driver/data/AddBridge/SimpleTest/text.txt
+++ /dev/null
@@ -1,6 +0,0 @@
-1	AATAGAAG
-2	AATAGCTT
-3	AATAGAAG
-4	AATAGCTT
-5	AATAGAAG
-6	AGAAGAAG
diff --git a/genomix/genomix-driver/src/main/java/edu/uci/ics/genomix/driver/GenomixDriver.java b/genomix/genomix-driver/src/main/java/edu/uci/ics/genomix/driver/GenomixDriver.java
index 0ca88ec..cd31ffe 100644
--- a/genomix/genomix-driver/src/main/java/edu/uci/ics/genomix/driver/GenomixDriver.java
+++ b/genomix/genomix-driver/src/main/java/edu/uci/ics/genomix/driver/GenomixDriver.java
@@ -186,12 +186,11 @@
 
     public void runGenomix(GenomixJobConf conf) throws NumberFormatException, HyracksException, Exception {
         KmerBytesWritable.setGlobalKmerLength(Integer.parseInt(conf.get(GenomixJobConf.KMER_LENGTH)));
-        GenomixMiniCluster testCluster = new GenomixMiniCluster();
         jobs = new ArrayList<PregelixJob>();
         stepNum = 0;
         boolean runLocal = Boolean.parseBoolean(conf.get(GenomixJobConf.RUN_LOCAL));
         if (runLocal)
-            testCluster.setUp(conf);
+            GenomixMiniCluster.init(conf);
         
         String localInput = conf.get(GenomixJobConf.LOCAL_INPUT_DIR);
         if (localInput != null) {
@@ -272,7 +271,7 @@
             FileSystem.get(conf).rename(new Path(curOutput), new Path(GenomixJobConf.FINAL_OUTPUT_DIR));
 
         if (runLocal)
-            testCluster.tearDown();
+            GenomixMiniCluster.deinit();
     }
 
     public static void main(String[] args) throws CmdLineException, NumberFormatException, HyracksException, Exception {
@@ -282,7 +281,7 @@
                 //                            "-inputDir", "/home/wbiesing/code/hyracks/genomix/genomix-driver/graphbuild.binmerge",
 //                "-localInput", "../genomix-pregelix/data/TestSet/PathMerge/CyclePath/bin/part-00000", 
                 "-pipelineOrder", "BUILD" };
-        GenomixJobConf conf = GenomixJobConf.fromArguments(args);
+        GenomixJobConf conf = GenomixJobConf.fromArguments(myArgs);
         GenomixDriver driver = new GenomixDriver();
         driver.runGenomix(conf);
     }