diff --git a/genomix/genomix-hyracks/src/main/resources/scripts/genomix b/genomix/genomix-hyracks/src/main/resources/scripts/genomix
index bdd7f20..239a46c 100644
--- a/genomix/genomix-hyracks/src/main/resources/scripts/genomix
+++ b/genomix/genomix-hyracks/src/main/resources/scripts/genomix
@@ -91,7 +91,7 @@
   REPO="$BASEDIR"/lib
 fi
 
-CLASSPATH=$CLASSPATH_PREFIX:"$BASEDIR"/etc:"$REPO"/hyracks-dataflow-std-0.2.3-SNAPSHOT.jar:"$REPO"/hyracks-api-0.2.3-SNAPSHOT.jar:"$REPO"/json-20090211.jar:"$REPO"/httpclient-4.1-alpha2.jar:"$REPO"/httpcore-4.1-beta1.jar:"$REPO"/commons-logging-1.1.1.jar:"$REPO"/commons-codec-1.4.jar:"$REPO"/args4j-2.0.12.jar:"$REPO"/commons-lang3-3.1.jar:"$REPO"/hyracks-dataflow-common-0.2.3-SNAPSHOT.jar:"$REPO"/hyracks-data-std-0.2.3-SNAPSHOT.jar:"$REPO"/hyracks-control-cc-0.2.3-SNAPSHOT.jar:"$REPO"/hyracks-control-common-0.2.3-SNAPSHOT.jar:"$REPO"/jetty-server-8.0.0.RC0.jar:"$REPO"/servlet-api-3.0.20100224.jar:"$REPO"/jetty-continuation-8.0.0.RC0.jar:"$REPO"/jetty-http-8.0.0.RC0.jar:"$REPO"/jetty-io-8.0.0.RC0.jar:"$REPO"/jetty-webapp-8.0.0.RC0.jar:"$REPO"/jetty-xml-8.0.0.RC0.jar:"$REPO"/jetty-util-8.0.0.RC0.jar:"$REPO"/jetty-servlet-8.0.0.RC0.jar:"$REPO"/jetty-security-8.0.0.RC0.jar:"$REPO"/wicket-core-1.5.2.jar:"$REPO"/wicket-util-1.5.2.jar:"$REPO"/wicket-request-1.5.2.jar:"$REPO"/slf4j-api-1.6.1.jar:"$REPO"/slf4j-jcl-1.6.3.jar:"$REPO"/hyracks-control-nc-0.2.3-SNAPSHOT.jar:"$REPO"/dcache-client-0.0.1.jar:"$REPO"/jetty-client-8.0.0.M0.jar:"$REPO"/hyracks-net-0.2.3-SNAPSHOT.jar:"$REPO"/commons-io-1.3.1.jar:"$REPO"/hyracks-ipc-0.2.3-SNAPSHOT.jar:"$REPO"/genomix-0.2.3-SNAPSHOT.pom
+CLASSPATH=$CLASSPATH_PREFIX:"$BASEDIR"/etc:"$REPO"/hyracks-dataflow-std-0.2.3-SNAPSHOT.jar:"$REPO"/hyracks-api-0.2.3-SNAPSHOT.jar:"$REPO"/json-20090211.jar:"$REPO"/httpclient-4.1-alpha2.jar:"$REPO"/httpcore-4.1-beta1.jar:"$REPO"/commons-logging-1.1.1.jar:"$REPO"/args4j-2.0.12.jar:"$REPO"/commons-lang3-3.1.jar:"$REPO"/hyracks-dataflow-common-0.2.3-SNAPSHOT.jar:"$REPO"/hyracks-data-std-0.2.3-SNAPSHOT.jar:"$REPO"/hyracks-control-cc-0.2.3-SNAPSHOT.jar:"$REPO"/hyracks-control-common-0.2.3-SNAPSHOT.jar:"$REPO"/jetty-server-8.0.0.RC0.jar:"$REPO"/servlet-api-3.0.20100224.jar:"$REPO"/jetty-continuation-8.0.0.RC0.jar:"$REPO"/jetty-http-8.0.0.RC0.jar:"$REPO"/jetty-io-8.0.0.RC0.jar:"$REPO"/jetty-webapp-8.0.0.RC0.jar:"$REPO"/jetty-xml-8.0.0.RC0.jar:"$REPO"/jetty-util-8.0.0.RC0.jar:"$REPO"/jetty-servlet-8.0.0.RC0.jar:"$REPO"/jetty-security-8.0.0.RC0.jar:"$REPO"/wicket-core-1.5.2.jar:"$REPO"/wicket-util-1.5.2.jar:"$REPO"/wicket-request-1.5.2.jar:"$REPO"/slf4j-api-1.6.1.jar:"$REPO"/slf4j-jcl-1.6.3.jar:"$REPO"/hyracks-control-nc-0.2.3-SNAPSHOT.jar:"$REPO"/dcache-client-0.0.1.jar:"$REPO"/jetty-client-8.0.0.M0.jar:"$REPO"/hyracks-net-0.2.3-SNAPSHOT.jar:"$REPO"/commons-io-1.3.1.jar:"$REPO"/hyracks-ipc-0.2.3-SNAPSHOT.jar:"$REPO"/hadoop-core-0.20.2.jar:"$REPO"/commons-cli-1.2.jar:"$REPO"/xmlenc-0.52.jar:"$REPO"/commons-httpclient-3.0.1.jar:"$REPO"/commons-codec-1.3.jar:"$REPO"/commons-net-1.4.1.jar:"$REPO"/jetty-6.1.14.jar:"$REPO"/jetty-util-6.1.14.jar:"$REPO"/jasper-runtime-5.5.12.jar:"$REPO"/jasper-compiler-5.5.12.jar:"$REPO"/jsp-api-2.1-6.1.14.jar:"$REPO"/jsp-2.1-6.1.14.jar:"$REPO"/ant-1.6.5.jar:"$REPO"/commons-el-1.0.jar:"$REPO"/jets3t-0.7.1.jar:"$REPO"/servlet-api-2.5-6.1.14.jar:"$REPO"/kfs-0.3.jar:"$REPO"/hsqldb-1.8.0.10.jar:"$REPO"/oro-2.0.8.jar:"$REPO"/core-3.1.1.jar:"$REPO"/hadoop-test-0.20.2.jar:"$REPO"/ftplet-api-1.0.0.jar:"$REPO"/mina-core-2.0.0-M5.jar:"$REPO"/ftpserver-core-1.0.0.jar:"$REPO"/ftpserver-deprecated-1.0.0-M2.jar:"$REPO"/hyracks-hdfs-core-0.2.3-SNAPSHOT.jar:"$REPO"/hyracks-hdfs-0.20.2-0.2.3-SNAPSHOT.jar:"$REPO"/genomix-data-0.2.3-SNAPSHOT.jar:"$REPO"/genomix-hyracks-0.2.3-SNAPSHOT.jar
 
 # For Cygwin, switch paths to Windows format before running java
 if $cygwin; then
diff --git a/genomix/genomix-hyracks/src/main/resources/scripts/genomix.bat b/genomix/genomix-hyracks/src/main/resources/scripts/genomix.bat
index 1bd2098..abcafaf 100644
--- a/genomix/genomix-hyracks/src/main/resources/scripts/genomix.bat
+++ b/genomix/genomix-hyracks/src/main/resources/scripts/genomix.bat
@@ -71,7 +71,7 @@
 
 if "%REPO%"=="" set REPO=%BASEDIR%\lib
 
-set CLASSPATH="%BASEDIR%"\etc;"%REPO%"\hyracks-dataflow-std-0.2.3-SNAPSHOT.jar;"%REPO%"\hyracks-api-0.2.3-SNAPSHOT.jar;"%REPO%"\json-20090211.jar;"%REPO%"\httpclient-4.1-alpha2.jar;"%REPO%"\httpcore-4.1-beta1.jar;"%REPO%"\commons-logging-1.1.1.jar;"%REPO%"\commons-codec-1.4.jar;"%REPO%"\args4j-2.0.12.jar;"%REPO%"\commons-lang3-3.1.jar;"%REPO%"\hyracks-dataflow-common-0.2.3-SNAPSHOT.jar;"%REPO%"\hyracks-data-std-0.2.3-SNAPSHOT.jar;"%REPO%"\hyracks-control-cc-0.2.3-SNAPSHOT.jar;"%REPO%"\hyracks-control-common-0.2.3-SNAPSHOT.jar;"%REPO%"\jetty-server-8.0.0.RC0.jar;"%REPO%"\servlet-api-3.0.20100224.jar;"%REPO%"\jetty-continuation-8.0.0.RC0.jar;"%REPO%"\jetty-http-8.0.0.RC0.jar;"%REPO%"\jetty-io-8.0.0.RC0.jar;"%REPO%"\jetty-webapp-8.0.0.RC0.jar;"%REPO%"\jetty-xml-8.0.0.RC0.jar;"%REPO%"\jetty-util-8.0.0.RC0.jar;"%REPO%"\jetty-servlet-8.0.0.RC0.jar;"%REPO%"\jetty-security-8.0.0.RC0.jar;"%REPO%"\wicket-core-1.5.2.jar;"%REPO%"\wicket-util-1.5.2.jar;"%REPO%"\wicket-request-1.5.2.jar;"%REPO%"\slf4j-api-1.6.1.jar;"%REPO%"\slf4j-jcl-1.6.3.jar;"%REPO%"\hyracks-control-nc-0.2.3-SNAPSHOT.jar;"%REPO%"\dcache-client-0.0.1.jar;"%REPO%"\jetty-client-8.0.0.M0.jar;"%REPO%"\hyracks-net-0.2.3-SNAPSHOT.jar;"%REPO%"\commons-io-1.3.1.jar;"%REPO%"\hyracks-ipc-0.2.3-SNAPSHOT.jar;"%REPO%"\genomix-0.2.3-SNAPSHOT.pom
+set CLASSPATH="%BASEDIR%"\etc;"%REPO%"\hyracks-dataflow-std-0.2.3-SNAPSHOT.jar;"%REPO%"\hyracks-api-0.2.3-SNAPSHOT.jar;"%REPO%"\json-20090211.jar;"%REPO%"\httpclient-4.1-alpha2.jar;"%REPO%"\httpcore-4.1-beta1.jar;"%REPO%"\commons-logging-1.1.1.jar;"%REPO%"\args4j-2.0.12.jar;"%REPO%"\commons-lang3-3.1.jar;"%REPO%"\hyracks-dataflow-common-0.2.3-SNAPSHOT.jar;"%REPO%"\hyracks-data-std-0.2.3-SNAPSHOT.jar;"%REPO%"\hyracks-control-cc-0.2.3-SNAPSHOT.jar;"%REPO%"\hyracks-control-common-0.2.3-SNAPSHOT.jar;"%REPO%"\jetty-server-8.0.0.RC0.jar;"%REPO%"\servlet-api-3.0.20100224.jar;"%REPO%"\jetty-continuation-8.0.0.RC0.jar;"%REPO%"\jetty-http-8.0.0.RC0.jar;"%REPO%"\jetty-io-8.0.0.RC0.jar;"%REPO%"\jetty-webapp-8.0.0.RC0.jar;"%REPO%"\jetty-xml-8.0.0.RC0.jar;"%REPO%"\jetty-util-8.0.0.RC0.jar;"%REPO%"\jetty-servlet-8.0.0.RC0.jar;"%REPO%"\jetty-security-8.0.0.RC0.jar;"%REPO%"\wicket-core-1.5.2.jar;"%REPO%"\wicket-util-1.5.2.jar;"%REPO%"\wicket-request-1.5.2.jar;"%REPO%"\slf4j-api-1.6.1.jar;"%REPO%"\slf4j-jcl-1.6.3.jar;"%REPO%"\hyracks-control-nc-0.2.3-SNAPSHOT.jar;"%REPO%"\dcache-client-0.0.1.jar;"%REPO%"\jetty-client-8.0.0.M0.jar;"%REPO%"\hyracks-net-0.2.3-SNAPSHOT.jar;"%REPO%"\commons-io-1.3.1.jar;"%REPO%"\hyracks-ipc-0.2.3-SNAPSHOT.jar;"%REPO%"\hadoop-core-0.20.2.jar;"%REPO%"\commons-cli-1.2.jar;"%REPO%"\xmlenc-0.52.jar;"%REPO%"\commons-httpclient-3.0.1.jar;"%REPO%"\commons-codec-1.3.jar;"%REPO%"\commons-net-1.4.1.jar;"%REPO%"\jetty-6.1.14.jar;"%REPO%"\jetty-util-6.1.14.jar;"%REPO%"\jasper-runtime-5.5.12.jar;"%REPO%"\jasper-compiler-5.5.12.jar;"%REPO%"\jsp-api-2.1-6.1.14.jar;"%REPO%"\jsp-2.1-6.1.14.jar;"%REPO%"\ant-1.6.5.jar;"%REPO%"\commons-el-1.0.jar;"%REPO%"\jets3t-0.7.1.jar;"%REPO%"\servlet-api-2.5-6.1.14.jar;"%REPO%"\kfs-0.3.jar;"%REPO%"\hsqldb-1.8.0.10.jar;"%REPO%"\oro-2.0.8.jar;"%REPO%"\core-3.1.1.jar;"%REPO%"\hadoop-test-0.20.2.jar;"%REPO%"\ftplet-api-1.0.0.jar;"%REPO%"\mina-core-2.0.0-M5.jar;"%REPO%"\ftpserver-core-1.0.0.jar;"%REPO%"\ftpserver-deprecated-1.0.0-M2.jar;"%REPO%"\hyracks-hdfs-core-0.2.3-SNAPSHOT.jar;"%REPO%"\hyracks-hdfs-0.20.2-0.2.3-SNAPSHOT.jar;"%REPO%"\genomix-data-0.2.3-SNAPSHOT.jar;"%REPO%"\genomix-hyracks-0.2.3-SNAPSHOT.jar
 goto endInit
 
 @REM Reaching here means variables are defined and arguments have been captured
diff --git a/genomix/genomix-hyracks/src/main/resources/scripts/startcc.sh b/genomix/genomix-hyracks/src/main/resources/scripts/startcc.sh
index 93967e7..63b1aca 100644
--- a/genomix/genomix-hyracks/src/main/resources/scripts/startcc.sh
+++ b/genomix/genomix-hyracks/src/main/resources/scripts/startcc.sh
@@ -10,11 +10,11 @@
 
 #Remove the temp dir
 #rm -rf $CCTMP_DIR
-mkdir $CCTMP_DIR
+mkdir -p $CCTMP_DIR
 
 #Remove the logs dir
 #rm -rf $CCLOGS_DIR
-mkdir $CCLOGS_DIR
+mkdir -p $CCLOGS_DIR
 
 #Export JAVA_HOME and JAVA_OPTS
 export JAVA_HOME=$JAVA_HOME
diff --git a/genomix/genomix-hyracks/src/main/resources/scripts/startnc.sh b/genomix/genomix-hyracks/src/main/resources/scripts/startnc.sh
index ceaa7bc..5397244 100644
--- a/genomix/genomix-hyracks/src/main/resources/scripts/startnc.sh
+++ b/genomix/genomix-hyracks/src/main/resources/scripts/startnc.sh
@@ -12,11 +12,11 @@
 #Clean up temp dir
 
 #rm -rf $NCTMP_DIR
-mkdir $NCTMP_DIR
+mkdir -p $NCTMP_DIR
 
 #Clean up log dir
 #rm -rf $NCLOGS_DIR
-mkdir $NCLOGS_DIR
+mkdir -p $NCLOGS_DIR
 
 
 #Clean up I/O working dir
@@ -24,7 +24,7 @@
 for io_dir in $io_dirs
 do
 	#rm -rf $io_dir
-	mkdir $io_dir
+	mkdir -p $io_dir
 done
 
 #Set JAVA_HOME