diff --git a/genomix/HyracksCodeFormatProfile.xml b/genomix/genomix-core/HyracksCodeFormatProfile.xml
similarity index 100%
rename from genomix/HyracksCodeFormatProfile.xml
rename to genomix/genomix-core/HyracksCodeFormatProfile.xml
diff --git a/genomix/pom.xml b/genomix/genomix-core/pom.xml
similarity index 100%
rename from genomix/pom.xml
rename to genomix/genomix-core/pom.xml
diff --git a/genomix/src/main/assembly/binary-assembly.xml b/genomix/genomix-core/src/main/assembly/binary-assembly.xml
similarity index 100%
rename from genomix/src/main/assembly/binary-assembly.xml
rename to genomix/genomix-core/src/main/assembly/binary-assembly.xml
diff --git a/genomix/src/main/java/edu/uci/ics/genomix/data/normalizers/Integer64NormalizedKeyComputerFactory.java b/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/data/normalizers/Integer64NormalizedKeyComputerFactory.java
similarity index 100%
rename from genomix/src/main/java/edu/uci/ics/genomix/data/normalizers/Integer64NormalizedKeyComputerFactory.java
rename to genomix/genomix-core/src/main/java/edu/uci/ics/genomix/data/normalizers/Integer64NormalizedKeyComputerFactory.java
diff --git a/genomix/src/main/java/edu/uci/ics/genomix/data/partition/KmerHashPartitioncomputerFactory.java b/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/data/partition/KmerHashPartitioncomputerFactory.java
similarity index 100%
rename from genomix/src/main/java/edu/uci/ics/genomix/data/partition/KmerHashPartitioncomputerFactory.java
rename to genomix/genomix-core/src/main/java/edu/uci/ics/genomix/data/partition/KmerHashPartitioncomputerFactory.java
diff --git a/genomix/src/main/java/edu/uci/ics/genomix/data/serde/ByteSerializerDeserializer.java b/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/data/serde/ByteSerializerDeserializer.java
similarity index 100%
rename from genomix/src/main/java/edu/uci/ics/genomix/data/serde/ByteSerializerDeserializer.java
rename to genomix/genomix-core/src/main/java/edu/uci/ics/genomix/data/serde/ByteSerializerDeserializer.java
diff --git a/genomix/src/main/java/edu/uci/ics/genomix/data/std/accessors/LongBinaryHashFunctionFamily.java b/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/data/std/accessors/LongBinaryHashFunctionFamily.java
similarity index 100%
rename from genomix/src/main/java/edu/uci/ics/genomix/data/std/accessors/LongBinaryHashFunctionFamily.java
rename to genomix/genomix-core/src/main/java/edu/uci/ics/genomix/data/std/accessors/LongBinaryHashFunctionFamily.java
diff --git a/genomix/src/main/java/edu/uci/ics/genomix/data/std/accessors/LongHashFunctionFamily.java b/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/data/std/accessors/LongHashFunctionFamily.java
similarity index 100%
rename from genomix/src/main/java/edu/uci/ics/genomix/data/std/accessors/LongHashFunctionFamily.java
rename to genomix/genomix-core/src/main/java/edu/uci/ics/genomix/data/std/accessors/LongHashFunctionFamily.java
diff --git a/genomix/src/main/java/edu/uci/ics/genomix/dataflow/ConnectorPolicyAssignmentPolicy.java b/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/ConnectorPolicyAssignmentPolicy.java
similarity index 100%
rename from genomix/src/main/java/edu/uci/ics/genomix/dataflow/ConnectorPolicyAssignmentPolicy.java
rename to genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/ConnectorPolicyAssignmentPolicy.java
diff --git a/genomix/src/main/java/edu/uci/ics/genomix/dataflow/FileScanDescriptor.java b/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/FileScanDescriptor.java
similarity index 100%
rename from genomix/src/main/java/edu/uci/ics/genomix/dataflow/FileScanDescriptor.java
rename to genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/FileScanDescriptor.java
diff --git a/genomix/src/main/java/edu/uci/ics/genomix/dataflow/GenKmerDescriptor.java b/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/GenKmerDescriptor.java
similarity index 100%
rename from genomix/src/main/java/edu/uci/ics/genomix/dataflow/GenKmerDescriptor.java
rename to genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/GenKmerDescriptor.java
diff --git a/genomix/src/main/java/edu/uci/ics/genomix/dataflow/KmerSplitOperatorNodePushable.java b/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/KmerSplitOperatorNodePushable.java
similarity index 100%
rename from genomix/src/main/java/edu/uci/ics/genomix/dataflow/KmerSplitOperatorNodePushable.java
rename to genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/KmerSplitOperatorNodePushable.java
diff --git a/genomix/src/main/java/edu/uci/ics/genomix/dataflow/SplitFrame.java b/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/SplitFrame.java
similarity index 100%
rename from genomix/src/main/java/edu/uci/ics/genomix/dataflow/SplitFrame.java
rename to genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/SplitFrame.java
diff --git a/genomix/src/main/java/edu/uci/ics/genomix/dataflow/Tester.java b/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/Tester.java
similarity index 100%
rename from genomix/src/main/java/edu/uci/ics/genomix/dataflow/Tester.java
rename to genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/Tester.java
diff --git a/genomix/src/main/java/edu/uci/ics/genomix/dataflow/aggregators/DistributedMergeLmerAggregateFactory.java b/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/aggregators/DistributedMergeLmerAggregateFactory.java
similarity index 100%
rename from genomix/src/main/java/edu/uci/ics/genomix/dataflow/aggregators/DistributedMergeLmerAggregateFactory.java
rename to genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/aggregators/DistributedMergeLmerAggregateFactory.java
diff --git a/genomix/src/main/java/edu/uci/ics/genomix/dataflow/aggregators/MergeKmerAggregateFactory.java b/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/aggregators/MergeKmerAggregateFactory.java
similarity index 100%
rename from genomix/src/main/java/edu/uci/ics/genomix/dataflow/aggregators/MergeKmerAggregateFactory.java
rename to genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/aggregators/MergeKmerAggregateFactory.java
diff --git a/genomix/src/main/resources/conf/cluster.properties b/genomix/genomix-core/src/main/resources/conf/cluster.properties
similarity index 96%
rename from genomix/src/main/resources/conf/cluster.properties
rename to genomix/genomix-core/src/main/resources/conf/cluster.properties
index c9e87f0..5b2b757 100644
--- a/genomix/src/main/resources/conf/cluster.properties
+++ b/genomix/genomix-core/src/main/resources/conf/cluster.properties
@@ -5,7 +5,7 @@
 CC_CLUSTERPORT=1099
 
 #The directory of hyracks binaries
-HYRACKS_HOME="../../../hyracks"
+HYRACKS_HOME="../../../../hyracks"
 
 #The tmp directory for cc to install jars
 CCTMP_DIR=/tmp/t1
diff --git a/genomix/src/main/resources/conf/debugnc.properties b/genomix/genomix-core/src/main/resources/conf/debugnc.properties
similarity index 100%
rename from genomix/src/main/resources/conf/debugnc.properties
rename to genomix/genomix-core/src/main/resources/conf/debugnc.properties
diff --git a/genomix/src/main/resources/conf/master b/genomix/genomix-core/src/main/resources/conf/master
similarity index 100%
rename from genomix/src/main/resources/conf/master
rename to genomix/genomix-core/src/main/resources/conf/master
diff --git a/genomix/src/main/resources/conf/slaves b/genomix/genomix-core/src/main/resources/conf/slaves
similarity index 100%
rename from genomix/src/main/resources/conf/slaves
rename to genomix/genomix-core/src/main/resources/conf/slaves
diff --git a/genomix/src/main/resources/scripts/genomix b/genomix/genomix-core/src/main/resources/scripts/genomix
similarity index 100%
rename from genomix/src/main/resources/scripts/genomix
rename to genomix/genomix-core/src/main/resources/scripts/genomix
diff --git a/genomix/src/main/resources/scripts/genomix.bat b/genomix/genomix-core/src/main/resources/scripts/genomix.bat
similarity index 100%
rename from genomix/src/main/resources/scripts/genomix.bat
rename to genomix/genomix-core/src/main/resources/scripts/genomix.bat
diff --git a/genomix/src/main/resources/scripts/getip.sh b/genomix/genomix-core/src/main/resources/scripts/getip.sh
similarity index 100%
rename from genomix/src/main/resources/scripts/getip.sh
rename to genomix/genomix-core/src/main/resources/scripts/getip.sh
diff --git a/genomix/src/main/resources/scripts/startAllNCs.sh b/genomix/genomix-core/src/main/resources/scripts/startAllNCs.sh
similarity index 100%
rename from genomix/src/main/resources/scripts/startAllNCs.sh
rename to genomix/genomix-core/src/main/resources/scripts/startAllNCs.sh
diff --git a/genomix/src/main/resources/scripts/startCluster.sh b/genomix/genomix-core/src/main/resources/scripts/startCluster.sh
similarity index 100%
rename from genomix/src/main/resources/scripts/startCluster.sh
rename to genomix/genomix-core/src/main/resources/scripts/startCluster.sh
diff --git a/genomix/src/main/resources/scripts/startDebugNc.sh b/genomix/genomix-core/src/main/resources/scripts/startDebugNc.sh
similarity index 100%
rename from genomix/src/main/resources/scripts/startDebugNc.sh
rename to genomix/genomix-core/src/main/resources/scripts/startDebugNc.sh
diff --git a/genomix/src/main/resources/scripts/startcc.sh b/genomix/genomix-core/src/main/resources/scripts/startcc.sh
similarity index 100%
rename from genomix/src/main/resources/scripts/startcc.sh
rename to genomix/genomix-core/src/main/resources/scripts/startcc.sh
diff --git a/genomix/src/main/resources/scripts/startnc.sh b/genomix/genomix-core/src/main/resources/scripts/startnc.sh
similarity index 100%
rename from genomix/src/main/resources/scripts/startnc.sh
rename to genomix/genomix-core/src/main/resources/scripts/startnc.sh
diff --git a/genomix/src/main/resources/scripts/stopAllNCs.sh b/genomix/genomix-core/src/main/resources/scripts/stopAllNCs.sh
similarity index 100%
rename from genomix/src/main/resources/scripts/stopAllNCs.sh
rename to genomix/genomix-core/src/main/resources/scripts/stopAllNCs.sh
diff --git a/genomix/src/main/resources/scripts/stopCluster.sh b/genomix/genomix-core/src/main/resources/scripts/stopCluster.sh
similarity index 100%
rename from genomix/src/main/resources/scripts/stopCluster.sh
rename to genomix/genomix-core/src/main/resources/scripts/stopCluster.sh
diff --git a/genomix/src/main/resources/scripts/stopcc.sh b/genomix/genomix-core/src/main/resources/scripts/stopcc.sh
similarity index 100%
rename from genomix/src/main/resources/scripts/stopcc.sh
rename to genomix/genomix-core/src/main/resources/scripts/stopcc.sh
diff --git a/genomix/src/main/resources/scripts/stopnc.sh b/genomix/genomix-core/src/main/resources/scripts/stopnc.sh
similarity index 100%
rename from genomix/src/main/resources/scripts/stopnc.sh
rename to genomix/genomix-core/src/main/resources/scripts/stopnc.sh
diff --git a/hadoop/actual/conf.xml b/genomix/genomix-hadoop/actual/conf.xml
similarity index 100%
rename from hadoop/actual/conf.xml
rename to genomix/genomix-hadoop/actual/conf.xml
diff --git a/hadoop/actual/result2/.part-00000.crc b/genomix/genomix-hadoop/actual/result2/.part-00000.crc
similarity index 100%
rename from hadoop/actual/result2/.part-00000.crc
rename to genomix/genomix-hadoop/actual/result2/.part-00000.crc
Binary files differ
diff --git a/hadoop/actual/result2/part-00000 b/genomix/genomix-hadoop/actual/result2/part-00000
similarity index 100%
rename from hadoop/actual/result2/part-00000
rename to genomix/genomix-hadoop/actual/result2/part-00000
diff --git a/hadoop/data/webmap/text.txt b/genomix/genomix-hadoop/data/webmap/text.txt
similarity index 100%
rename from hadoop/data/webmap/text.txt
rename to genomix/genomix-hadoop/data/webmap/text.txt
diff --git a/hadoop/expected/result2 b/genomix/genomix-hadoop/expected/result2
similarity index 100%
rename from hadoop/expected/result2
rename to genomix/genomix-hadoop/expected/result2
diff --git a/hadoop/pom.xml b/genomix/genomix-hadoop/pom.xml
similarity index 100%
rename from hadoop/pom.xml
rename to genomix/genomix-hadoop/pom.xml
diff --git a/hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixCombiner.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixCombiner.java
similarity index 100%
rename from hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixCombiner.java
rename to genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixCombiner.java
diff --git a/hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixDriver.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixDriver.java
similarity index 100%
rename from hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixDriver.java
rename to genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixDriver.java
diff --git a/hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixMapper.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixMapper.java
similarity index 100%
rename from hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixMapper.java
rename to genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixMapper.java
diff --git a/hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixReducer.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixReducer.java
similarity index 100%
rename from hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixReducer.java
rename to genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixReducer.java
diff --git a/hadoop/src/main/java/edu/uci/ics/graphbuilding/ValueWritable.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/ValueWritable.java
similarity index 100%
rename from hadoop/src/main/java/edu/uci/ics/graphbuilding/ValueWritable.java
rename to genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/ValueWritable.java
diff --git a/hadoop/src/test/java/edu/uci/ics/graphbuilding/GraphBuildingTest.java b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/graphbuilding/GraphBuildingTest.java
similarity index 100%
rename from hadoop/src/test/java/edu/uci/ics/graphbuilding/GraphBuildingTest.java
rename to genomix/genomix-hadoop/src/test/java/edu/uci/ics/graphbuilding/GraphBuildingTest.java
diff --git a/hadoop/src/test/java/edu/uci/ics/utils/TestUtils.java b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/utils/TestUtils.java
similarity index 100%
rename from hadoop/src/test/java/edu/uci/ics/utils/TestUtils.java
rename to genomix/genomix-hadoop/src/test/java/edu/uci/ics/utils/TestUtils.java