diff --git a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/pmcommon/GenomixMiniClusterTest.java b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/pmcommon/GenomixMiniClusterTest.java
deleted file mode 100644
index 714d77e..0000000
--- a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/pmcommon/GenomixMiniClusterTest.java
+++ /dev/null
@@ -1,192 +0,0 @@
-package edu.uci.ics.genomix.hadoop.pmcommon;
-
-import java.io.BufferedWriter;
-import java.io.DataOutputStream;
-import java.io.File;
-import java.io.FileOutputStream;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.util.ArrayList;
-
-import org.apache.commons.io.FileUtils;
-import org.apache.hadoop.conf.Configuration;
-import org.apache.hadoop.fs.FileStatus;
-import org.apache.hadoop.fs.FileSystem;
-import org.apache.hadoop.fs.FileUtil;
-import org.apache.hadoop.fs.Path;
-import org.apache.hadoop.hdfs.MiniDFSCluster;
-import org.apache.hadoop.io.SequenceFile;
-import org.apache.hadoop.io.Writable;
-import org.apache.hadoop.mapred.JobConf;
-import org.apache.hadoop.mapred.MiniMRCluster;
-import org.apache.hadoop.util.ReflectionUtils;
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.BeforeClass;
-
-import edu.uci.ics.genomix.hyracks.driver.Driver;
-import edu.uci.ics.genomix.hyracks.job.GenomixJobConf;
-import edu.uci.ics.genomix.hyracks.test.TestUtils;
-import edu.uci.ics.hyracks.hdfs.utils.HyracksUtils;
-
-/*
- * A base class providing most of the boilerplate for Genomix-based tests
- */
-@SuppressWarnings("deprecation")
-public class GenomixMiniClusterTest {
-    protected int KMER_LENGTH = 5;
-    protected int READ_LENGTH = 8;
-
-    // subclass should modify this to include the HDFS directories that should be cleaned up
-    protected ArrayList<String> HDFS_PATHS = new ArrayList<String>();
-
-    protected static String EXPECTED_ROOT = "src/test/resources/expected/";
-    protected static String ACTUAL_ROOT = "src/test/resources/actual/";
-
-    protected static String HADOOP_CONF_ROOT = "src/test/resources/hadoop/conf/";
-
-    protected static MiniDFSCluster dfsCluster;
-    protected static MiniMRCluster mrCluster;
-    private static FileSystem dfs;
-    protected static JobConf conf = new JobConf();
-    protected static int numberOfNC = 1;
-    protected static int numPartitionPerMachine = 1;
-    protected static Driver driver;
-
-    @BeforeClass
-    public static void setUpMiniCluster() throws Exception {
-        cleanupStores();
-        startHDFS();
-        HyracksUtils.init();
-        FileUtils.forceMkdir(new File(ACTUAL_ROOT));
-        FileUtils.cleanDirectory(new File(ACTUAL_ROOT));
-        driver = new Driver(HyracksUtils.CC_HOST, HyracksUtils.TEST_HYRACKS_CC_CLIENT_PORT, numPartitionPerMachine);
-    }
-
-    /*
-     * Merge and copy a DFS directory to a local destination, converting to text if necessary. 
-     * Also locally store the binary-formatted result if available.
-     */
-    protected static void copyResultsToLocal(String hdfsSrcDir, String localDestFile, boolean resultsAreText,
-            Configuration conf) throws IOException {
-        if (resultsAreText) {
-            // for text files, just concatenate them together
-            FileUtil.copyMerge(FileSystem.get(conf), new Path(hdfsSrcDir), FileSystem.getLocal(new Configuration()),
-                    new Path(localDestFile), false, conf, null);
-        } else {
-            // file is binary
-//            // save the entire binary output dir
-//            FileUtil.copy(FileSystem.get(conf), new Path(hdfsSrcDir), FileSystem.getLocal(new Configuration()),
-//                    new Path(localDestFile + ".bindir"), false, conf);
-
-            // also load the Nodes and write them out as text locally. 
-            FileSystem lfs = FileSystem.getLocal(new Configuration());
-            lfs.mkdirs(new Path(localDestFile).getParent());
-            File filePathTo = new File(localDestFile);
-            BufferedWriter bw = new BufferedWriter(new FileWriter(filePathTo));
-
-            FileStatus[] files = dfs.globStatus(new Path(hdfsSrcDir + "*"));
-            SequenceFile.Reader reader = new SequenceFile.Reader(dfs, files[0].getPath(), conf);
-            String destBinDir = localDestFile.substring(0, localDestFile.lastIndexOf("."));
-//            FileUtil.copy(FileSystem.get(conf), new Path(hdfsSrcDir), FileSystem.getLocal(new Configuration()),
-//                    new Path(destBinDir), false, conf);
-            SequenceFile.Writer writer = new SequenceFile.Writer(lfs, new JobConf(), new Path(localDestFile
-                    + ".binmerge"), reader.getKeyClass(), reader.getValueClass());
-
-            Writable key = (Writable) ReflectionUtils.newInstance(reader.getKeyClass(), conf);
-            Writable value = (Writable) ReflectionUtils.newInstance(reader.getValueClass(), conf);
-
-            for (FileStatus f : files) {
-                if (f.getLen() == 0) {
-                    continue;
-                }
-                reader = new SequenceFile.Reader(dfs, f.getPath(), conf);
-                while (reader.next(key, value)) {
-                    if (key == null || value == null) {
-                        break;
-                    }
-                    bw.write(key.toString() + "\t" + value.toString());
-                    System.out.println(key.toString() + "\t" + value.toString());
-                    bw.newLine();
-                    writer.append(key, value);
-
-                }
-                reader.close();
-            }
-            writer.close();
-            bw.close();
-        }
-
-    }
-
-    protected static boolean checkResults(String expectedPath, String actualPath, int[] poslistField) throws Exception {
-        File dumped = new File(actualPath);
-        if (poslistField != null) {
-            TestUtils.compareWithUnSortedPosition(new File(expectedPath), dumped, poslistField);
-        } else {
-            TestUtils.compareWithSortedResult(new File(expectedPath), dumped);
-        }
-        return true;
-    }
-
-    protected static void cleanupStores() throws IOException {
-        FileUtils.forceMkdir(new File("teststore"));
-        FileUtils.forceMkdir(new File("build"));
-        FileUtils.cleanDirectory(new File("teststore"));
-        FileUtils.cleanDirectory(new File("build"));
-    }
-
-    protected static void startHDFS() throws IOException {
-        conf.addResource(new Path(HADOOP_CONF_ROOT + "core-site.xml"));
-        //        conf.addResource(new Path(HADOOP_CONF_ROOT + "mapred-site.xml"));
-        conf.addResource(new Path(HADOOP_CONF_ROOT + "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);
-        dfs = dfsCluster.getFileSystem();
-        mrCluster = new MiniMRCluster(4, dfs.getUri().toString(), 2);
-        System.out.println(dfs.getUri().toString());
-
-        DataOutputStream confOutput = new DataOutputStream(
-                new FileOutputStream(new File(HADOOP_CONF_ROOT + "conf.xml")));
-        conf.writeXml(confOutput);
-        confOutput.close();
-    }
-
-    protected static void copyLocalToDFS(String localSrc, String hdfsDest) throws IOException {
-        Path dest = new Path(hdfsDest);
-        dfs.mkdirs(dest);
-        dfs.copyFromLocalFile(new Path(localSrc), dest);
-    }
-
-    /*
-     * Remove the local "actual" folder and any hdfs folders in use by this test
-     */
-    public void cleanUpOutput() throws IOException {
-//        // local cleanup
-//        FileSystem lfs = FileSystem.getLocal(new Configuration());
-//        if (lfs.exists(new Path(ACTUAL_ROOT))) {
-//            lfs.delete(new Path(ACTUAL_ROOT), true);
-//        }
-        // dfs cleanup
-        for (String path : HDFS_PATHS) {
-            if (dfs.exists(new Path(path))) {
-                dfs.delete(new Path(path), true);
-            }
-        }
-    }
-
-    @AfterClass
-    public static void tearDown() throws Exception {
-        HyracksUtils.deinit();
-        cleanupHDFS();
-    }
-
-    protected static void cleanupHDFS() throws Exception {
-        dfsCluster.shutdown();
-        mrCluster.shutdown();
-    }
-}