remove unrelated files
diff --git a/genomix/genomix-data/target/classes/META-INF/MANIFEST.MF b/genomix/genomix-data/target/classes/META-INF/MANIFEST.MF
deleted file mode 100644
index da18195..0000000
--- a/genomix/genomix-data/target/classes/META-INF/MANIFEST.MF
+++ /dev/null
@@ -1,5 +0,0 @@
-Manifest-Version: 1.0
-Built-By: jiajianfeng
-Build-Jdk: 1.6.0_43
-Created-By: Maven Integration for Eclipse
-
diff --git a/genomix/genomix-data/target/classes/META-INF/maven/edu.uci.ics.hyracks/genomix-data/pom.properties b/genomix/genomix-data/target/classes/META-INF/maven/edu.uci.ics.hyracks/genomix-data/pom.properties
deleted file mode 100644
index e59f3fc..0000000
--- a/genomix/genomix-data/target/classes/META-INF/maven/edu.uci.ics.hyracks/genomix-data/pom.properties
+++ /dev/null
@@ -1,7 +0,0 @@
-#Generated by Maven Integration for Eclipse
-#Fri Apr 12 22:12:36 PDT 2013
-version=0.2.4-SNAPSHOT
-groupId=edu.uci.ics.hyracks
-m2e.projectName=genomix-data
-m2e.projectLocation=/Users/jiajianfeng/workplace/code/asterix/fullstack/genomix/genomix-data
-artifactId=genomix-data
diff --git a/genomix/genomix-data/target/classes/META-INF/maven/edu.uci.ics.hyracks/genomix-data/pom.xml b/genomix/genomix-data/target/classes/META-INF/maven/edu.uci.ics.hyracks/genomix-data/pom.xml
deleted file mode 100644
index 5ce538f..0000000
--- a/genomix/genomix-data/target/classes/META-INF/maven/edu.uci.ics.hyracks/genomix-data/pom.xml
+++ /dev/null
@@ -1,47 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
- <modelVersion>4.0.0</modelVersion>
- <artifactId>genomix-data</artifactId>
- <name>genomix-data</name>
-
- <parent>
- <groupId>edu.uci.ics.hyracks</groupId>
- <artifactId>genomix</artifactId>
- <version>0.2.4-SNAPSHOT</version>
- </parent>
-
- <properties>
- <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
- </properties>
-
- <build>
- <plugins>
- <plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-compiler-plugin</artifactId>
- <version>2.0.2</version>
- <configuration>
- <source>1.7</source>
- <target>1.7</target>
- <fork>true</fork>
- </configuration>
- </plugin>
- </plugins>
- </build>
-
-
- <dependencies>
- <dependency>
- <groupId>junit</groupId>
- <artifactId>junit</artifactId>
- <version>4.8.1</version>
- <scope>test</scope>
- </dependency>
- <dependency>
- <groupId>org.apache.hadoop</groupId>
- <artifactId>hadoop-core</artifactId>
- <version>0.20.2</version>
- </dependency>
- </dependencies>
-</project>
diff --git a/genomix/genomix-data/target/classes/conf/cluster.properties b/genomix/genomix-data/target/classes/conf/cluster.properties
deleted file mode 100644
index eabd81b..0000000
--- a/genomix/genomix-data/target/classes/conf/cluster.properties
+++ /dev/null
@@ -1,40 +0,0 @@
-#The CC port for Hyracks clients
-CC_CLIENTPORT=3099
-
-#The CC port for Hyracks cluster management
-CC_CLUSTERPORT=1099
-
-#The directory of hyracks binaries
-HYRACKS_HOME="../../../../hyracks"
-
-#The tmp directory for cc to install jars
-CCTMP_DIR=/tmp/t1
-
-#The tmp directory for nc to install jars
-NCTMP_DIR=/tmp/t2
-
-#The directory to put cc logs
-CCLOGS_DIR=$CCTMP_DIR/logs
-
-#The directory to put nc logs
-NCLOGS_DIR=$NCTMP_DIR/logs
-
-#Comma separated I/O directories for the spilling of external sort
-IO_DIRS="/tmp/t3,/tmp/t4"
-
-#The JAVA_HOME
-JAVA_HOME=$JAVA_HOME
-
-#HADOOP_HOME
-CLASSPATH="${HADOOP_HOME}:${CLASSPATH}:."
-
-#The frame size of the internal dataflow engine
-FRAME_SIZE=65536
-
-#CC JAVA_OPTS
-CCJAVA_OPTS="-Xdebug -Xrunjdwp:transport=dt_socket,address=7001,server=y,suspend=n -Xmx1g -Djava.util.logging.config.file=logging.properties"
-# Yourkit option: -agentpath:/grid/0/dev/vborkar/tools/yjp-10.0.4/bin/linux-x86-64/libyjpagent.so=port=20001"
-
-#NC JAVA_OPTS
-NCJAVA_OPTS="-Xdebug -Xrunjdwp:transport=dt_socket,address=7002,server=y,suspend=n -Xmx10g -Djava.util.logging.config.file=logging.properties"
-
diff --git a/genomix/genomix-data/target/classes/conf/debugnc.properties b/genomix/genomix-data/target/classes/conf/debugnc.properties
deleted file mode 100644
index 27afa26..0000000
--- a/genomix/genomix-data/target/classes/conf/debugnc.properties
+++ /dev/null
@@ -1,12 +0,0 @@
-#The tmp directory for nc to install jars
-NCTMP_DIR2=/tmp/t-1
-
-#The directory to put nc logs
-NCLOGS_DIR2=$NCTMP_DIR/logs
-
-#Comma separated I/O directories for the spilling of external sort
-IO_DIRS2="/tmp/t-2,/tmp/t-3"
-
-#NC JAVA_OPTS
-NCJAVA_OPTS2="-Xdebug -Xrunjdwp:transport=dt_socket,address=7003,server=y,suspend=n -Xmx1g -Djava.util.logging.config.file=logging.properties"
-
diff --git a/genomix/genomix-data/target/classes/conf/master b/genomix/genomix-data/target/classes/conf/master
deleted file mode 100644
index 2fbb50c..0000000
--- a/genomix/genomix-data/target/classes/conf/master
+++ /dev/null
@@ -1 +0,0 @@
-localhost
diff --git a/genomix/genomix-data/target/classes/conf/slaves b/genomix/genomix-data/target/classes/conf/slaves
deleted file mode 100644
index 2fbb50c..0000000
--- a/genomix/genomix-data/target/classes/conf/slaves
+++ /dev/null
@@ -1 +0,0 @@
-localhost
diff --git a/genomix/genomix-data/target/classes/edu/uci/ics/genomix/type/Kmer$GENE_CODE.class b/genomix/genomix-data/target/classes/edu/uci/ics/genomix/type/Kmer$GENE_CODE.class
deleted file mode 100644
index 623f0c2..0000000
--- a/genomix/genomix-data/target/classes/edu/uci/ics/genomix/type/Kmer$GENE_CODE.class
+++ /dev/null
Binary files differ
diff --git a/genomix/genomix-data/target/classes/edu/uci/ics/genomix/type/Kmer.class b/genomix/genomix-data/target/classes/edu/uci/ics/genomix/type/Kmer.class
deleted file mode 100644
index ffeb20f..0000000
--- a/genomix/genomix-data/target/classes/edu/uci/ics/genomix/type/Kmer.class
+++ /dev/null
Binary files differ
diff --git a/genomix/genomix-data/target/classes/edu/uci/ics/genomix/type/KmerBytesWritable$Comparator.class b/genomix/genomix-data/target/classes/edu/uci/ics/genomix/type/KmerBytesWritable$Comparator.class
deleted file mode 100644
index c94d38c..0000000
--- a/genomix/genomix-data/target/classes/edu/uci/ics/genomix/type/KmerBytesWritable$Comparator.class
+++ /dev/null
Binary files differ
diff --git a/genomix/genomix-data/target/classes/edu/uci/ics/genomix/type/KmerBytesWritable.class b/genomix/genomix-data/target/classes/edu/uci/ics/genomix/type/KmerBytesWritable.class
deleted file mode 100644
index 0620a64..0000000
--- a/genomix/genomix-data/target/classes/edu/uci/ics/genomix/type/KmerBytesWritable.class
+++ /dev/null
Binary files differ
diff --git a/genomix/genomix-data/target/classes/edu/uci/ics/genomix/type/KmerCountValue.class b/genomix/genomix-data/target/classes/edu/uci/ics/genomix/type/KmerCountValue.class
deleted file mode 100644
index 67f9303..0000000
--- a/genomix/genomix-data/target/classes/edu/uci/ics/genomix/type/KmerCountValue.class
+++ /dev/null
Binary files differ
diff --git a/genomix/genomix-data/target/classes/edu/uci/ics/genomix/type/KmerUtil.class b/genomix/genomix-data/target/classes/edu/uci/ics/genomix/type/KmerUtil.class
deleted file mode 100644
index 8324f12..0000000
--- a/genomix/genomix-data/target/classes/edu/uci/ics/genomix/type/KmerUtil.class
+++ /dev/null
Binary files differ
diff --git a/genomix/genomix-data/target/classes/scripts/genomix b/genomix/genomix-data/target/classes/scripts/genomix
deleted file mode 100644
index bdd7f20..0000000
--- a/genomix/genomix-data/target/classes/scripts/genomix
+++ /dev/null
@@ -1,113 +0,0 @@
-#!/bin/sh
-# ----------------------------------------------------------------------------
-# Copyright 2001-2006 The Apache Software Foundation.
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-# ----------------------------------------------------------------------------
-#
-# Copyright (c) 2001-2006 The Apache Software Foundation. All rights
-# reserved.
-
-
-# resolve links - $0 may be a softlink
-PRG="$0"
-
-while [ -h "$PRG" ]; do
- ls=`ls -ld "$PRG"`
- link=`expr "$ls" : '.*-> \(.*\)$'`
- if expr "$link" : '/.*' > /dev/null; then
- PRG="$link"
- else
- PRG=`dirname "$PRG"`/"$link"
- fi
-done
-
-PRGDIR=`dirname "$PRG"`
-BASEDIR=`cd "$PRGDIR/.." >/dev/null; pwd`
-
-
-
-# OS specific support. $var _must_ be set to either true or false.
-cygwin=false;
-darwin=false;
-case "`uname`" in
- CYGWIN*) cygwin=true ;;
- Darwin*) darwin=true
- if [ -z "$JAVA_VERSION" ] ; then
- JAVA_VERSION="CurrentJDK"
- else
- echo "Using Java version: $JAVA_VERSION"
- fi
- if [ -z "$JAVA_HOME" ] ; then
- JAVA_HOME=/System/Library/Frameworks/JavaVM.framework/Versions/${JAVA_VERSION}/Home
- fi
- ;;
-esac
-
-if [ -z "$JAVA_HOME" ] ; then
- if [ -r /etc/gentoo-release ] ; then
- JAVA_HOME=`java-config --jre-home`
- fi
-fi
-
-# For Cygwin, ensure paths are in UNIX format before anything is touched
-if $cygwin ; then
- [ -n "$JAVA_HOME" ] && JAVA_HOME=`cygpath --unix "$JAVA_HOME"`
- [ -n "$CLASSPATH" ] && CLASSPATH=`cygpath --path --unix "$CLASSPATH"`
-fi
-
-# If a specific java binary isn't specified search for the standard 'java' binary
-if [ -z "$JAVACMD" ] ; then
- if [ -n "$JAVA_HOME" ] ; then
- if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
- # IBM's JDK on AIX uses strange locations for the executables
- JAVACMD="$JAVA_HOME/jre/sh/java"
- else
- JAVACMD="$JAVA_HOME/bin/java"
- fi
- else
- JAVACMD=`which java`
- fi
-fi
-
-if [ ! -x "$JAVACMD" ] ; then
- echo "Error: JAVA_HOME is not defined correctly." 1>&2
- echo " We cannot execute $JAVACMD" 1>&2
- exit 1
-fi
-
-if [ -z "$REPO" ]
-then
- 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
-
-# For Cygwin, switch paths to Windows format before running java
-if $cygwin; then
- [ -n "$CLASSPATH" ] && CLASSPATH=`cygpath --path --windows "$CLASSPATH"`
- [ -n "$JAVA_HOME" ] && JAVA_HOME=`cygpath --path --windows "$JAVA_HOME"`
- [ -n "$HOME" ] && HOME=`cygpath --path --windows "$HOME"`
- [ -n "$BASEDIR" ] && BASEDIR=`cygpath --path --windows "$BASEDIR"`
- [ -n "$REPO" ] && REPO=`cygpath --path --windows "$REPO"`
-fi
-
-exec "$JAVACMD" $JAVA_OPTS \
- -classpath "$CLASSPATH" \
- -Dapp.name="genomix" \
- -Dapp.pid="$$" \
- -Dapp.repo="$REPO" \
- -Dapp.home="$BASEDIR" \
- -Dbasedir="$BASEDIR" \
- edu.uci.ics.genomix.driver.Driver \
- "$@"
diff --git a/genomix/genomix-data/target/classes/scripts/genomix.bat b/genomix/genomix-data/target/classes/scripts/genomix.bat
deleted file mode 100644
index 1bd2098..0000000
--- a/genomix/genomix-data/target/classes/scripts/genomix.bat
+++ /dev/null
@@ -1,108 +0,0 @@
-@REM ----------------------------------------------------------------------------
-@REM Copyright 2001-2006 The Apache Software Foundation.
-@REM
-@REM Licensed under the Apache License, Version 2.0 (the "License");
-@REM you may not use this file except in compliance with the License.
-@REM You may obtain a copy of the License at
-@REM
-@REM http://www.apache.org/licenses/LICENSE-2.0
-@REM
-@REM Unless required by applicable law or agreed to in writing, software
-@REM distributed under the License is distributed on an "AS IS" BASIS,
-@REM WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-@REM See the License for the specific language governing permissions and
-@REM limitations under the License.
-@REM ----------------------------------------------------------------------------
-@REM
-@REM Copyright (c) 2001-2006 The Apache Software Foundation. All rights
-@REM reserved.
-
-@echo off
-
-set ERROR_CODE=0
-
-:init
-@REM Decide how to startup depending on the version of windows
-
-@REM -- Win98ME
-if NOT "%OS%"=="Windows_NT" goto Win9xArg
-
-@REM set local scope for the variables with windows NT shell
-if "%OS%"=="Windows_NT" @setlocal
-
-@REM -- 4NT shell
-if "%eval[2+2]" == "4" goto 4NTArgs
-
-@REM -- Regular WinNT shell
-set CMD_LINE_ARGS=%*
-goto WinNTGetScriptDir
-
-@REM The 4NT Shell from jp software
-:4NTArgs
-set CMD_LINE_ARGS=%$
-goto WinNTGetScriptDir
-
-:Win9xArg
-@REM Slurp the command line arguments. This loop allows for an unlimited number
-@REM of arguments (up to the command line limit, anyway).
-set CMD_LINE_ARGS=
-:Win9xApp
-if %1a==a goto Win9xGetScriptDir
-set CMD_LINE_ARGS=%CMD_LINE_ARGS% %1
-shift
-goto Win9xApp
-
-:Win9xGetScriptDir
-set SAVEDIR=%CD%
-%0\
-cd %0\..\..
-set BASEDIR=%CD%
-cd %SAVEDIR%
-set SAVE_DIR=
-goto repoSetup
-
-:WinNTGetScriptDir
-set BASEDIR=%~dp0\..
-
-:repoSetup
-
-
-if "%JAVACMD%"=="" set JAVACMD=java
-
-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
-goto endInit
-
-@REM Reaching here means variables are defined and arguments have been captured
-:endInit
-
-%JAVACMD% %JAVA_OPTS% -classpath %CLASSPATH_PREFIX%;%CLASSPATH% -Dapp.name="genomix" -Dapp.repo="%REPO%" -Dapp.home="%BASEDIR%" -Dbasedir="%BASEDIR%" edu.uci.ics.genomix.driver.Driver %CMD_LINE_ARGS%
-if ERRORLEVEL 1 goto error
-goto end
-
-:error
-if "%OS%"=="Windows_NT" @endlocal
-set ERROR_CODE=%ERRORLEVEL%
-
-:end
-@REM set local scope for the variables with windows NT shell
-if "%OS%"=="Windows_NT" goto endNT
-
-@REM For old DOS remove the set variables from ENV - we assume they were not set
-@REM before we started - at least we don't leave any baggage around
-set CMD_LINE_ARGS=
-goto postExec
-
-:endNT
-@REM If error code is set to 1 then the endlocal was done already in :error.
-if %ERROR_CODE% EQU 0 @endlocal
-
-
-:postExec
-
-if "%FORCE_EXIT_ON_ERROR%" == "on" (
- if %ERROR_CODE% NEQ 0 exit %ERROR_CODE%
-)
-
-exit /B %ERROR_CODE%
diff --git a/genomix/genomix-data/target/classes/scripts/getip.sh b/genomix/genomix-data/target/classes/scripts/getip.sh
deleted file mode 100644
index e0cdf73..0000000
--- a/genomix/genomix-data/target/classes/scripts/getip.sh
+++ /dev/null
@@ -1,21 +0,0 @@
-#get the OS
-OS_NAME=`uname -a|awk '{print $1}'`
-LINUX_OS='Linux'
-
-if [ $OS_NAME = $LINUX_OS ];
-then
- #Get IP Address
- IPADDR=`/sbin/ifconfig eth0 | grep "inet " | awk '{print $2}' | cut -f 2 -d ':'`
- if [ "$IPADDR" = "" ]
- then
- IPADDR=`/sbin/ifconfig lo | grep "inet " | awk '{print $2}' | cut -f 2 -d ':'`
- fi
-else
- IPADDR=`/sbin/ifconfig en1 | grep "inet " | awk '{print $2}' | cut -f 2 -d ':'`
- if [ "$IPADDR" = "" ]
- then
- IPADDR=`/sbin/ifconfig lo0 | grep "inet " | awk '{print $2}' | cut -f 2 -d ':'`
- fi
-
-fi
-echo $IPADDR
diff --git a/genomix/genomix-data/target/classes/scripts/startAllNCs.sh b/genomix/genomix-data/target/classes/scripts/startAllNCs.sh
deleted file mode 100644
index 5e38c40..0000000
--- a/genomix/genomix-data/target/classes/scripts/startAllNCs.sh
+++ /dev/null
@@ -1,6 +0,0 @@
-GENOMIX_PATH=`pwd`
-
-for i in `cat conf/slaves`
-do
- ssh $i "cd ${GENOMIX_PATH}; bin/startnc.sh"
-done
diff --git a/genomix/genomix-data/target/classes/scripts/startCluster.sh b/genomix/genomix-data/target/classes/scripts/startCluster.sh
deleted file mode 100644
index 4727764..0000000
--- a/genomix/genomix-data/target/classes/scripts/startCluster.sh
+++ /dev/null
@@ -1,19 +0,0 @@
-bin/startcc.sh
-sleep 5
-bin/startAllNCs.sh
-
-. conf/cluster.properties
-# do we need to specify the version somewhere?
-hyrackcmd=`ls ${HYRACKS_HOME}/hyracks-cli/target/hyracks-cli-*-binary-assembly/bin/hyrackscli`
-# find zip file
-appzip=`ls $PWD/../genomix-*-binary-assembly.zip`
-
-[ -f $hyrackcmd ] || { echo "Hyracks commandline is missing"; exit -1;}
-[ -f $appzip ] || { echo "Genomix binary-assembly.zip is missing"; exit -1;}
-
-CCHOST_NAME=`cat conf/master`
-
-IPADDR=`bin/getip.sh`
-echo "connect to \"${IPADDR}:${CC_CLIENTPORT}\"; create application genomix \"$appzip\";" | $hyrackcmd
-echo ""
-
diff --git a/genomix/genomix-data/target/classes/scripts/startDebugNc.sh b/genomix/genomix-data/target/classes/scripts/startDebugNc.sh
deleted file mode 100644
index fe6cf27..0000000
--- a/genomix/genomix-data/target/classes/scripts/startDebugNc.sh
+++ /dev/null
@@ -1,50 +0,0 @@
-hostname
-
-#Get the IP address of the cc
-CCHOST_NAME=`cat conf/master`
-CURRENT_PATH=`pwd`
-CCHOST=`ssh ${CCHOST_NAME} "cd ${CURRENT_PATH}; bin/getip.sh"`
-
-#Import cluster properties
-. conf/cluster.properties
-. conf/debugnc.properties
-
-#Clean up temp dir
-
-rm -rf $NCTMP_DIR2
-mkdir $NCTMP_DIR2
-
-#Clean up log dir
-rm -rf $NCLOGS_DIR2
-mkdir $NCLOGS_DIR2
-
-
-#Clean up I/O working dir
-io_dirs=$(echo $IO_DIRS2 | tr "," "\n")
-for io_dir in $io_dirs
-do
- rm -rf $io_dir
- mkdir $io_dir
-done
-
-#Set JAVA_HOME
-export JAVA_HOME=$JAVA_HOME
-
-#Get OS
-IPADDR=`bin/getip.sh`
-
-#Get node ID
-NODEID=`hostname | cut -d '.' -f 1`
-NODEID=${NODEID}2
-
-#Set JAVA_OPTS
-export JAVA_OPTS=$NCJAVA_OPTS2
-
-cd $HYRACKS_HOME
-HYRACKS_HOME=`pwd`
-
-#Enter the temp dir
-cd $NCTMP_DIR2
-
-#Launch hyracks nc
-$HYRACKS_HOME/hyracks-server/target/appassembler/bin/hyracksnc -cc-host $CCHOST -cc-port $CC_CLUSTERPORT -cluster-net-ip-address $IPADDR -data-ip-address $IPADDR -node-id $NODEID -iodevices "${IO_DIRS2}" &> $NCLOGS_DIR2/$NODEID.log &
diff --git a/genomix/genomix-data/target/classes/scripts/startcc.sh b/genomix/genomix-data/target/classes/scripts/startcc.sh
deleted file mode 100644
index fe2551d..0000000
--- a/genomix/genomix-data/target/classes/scripts/startcc.sh
+++ /dev/null
@@ -1,25 +0,0 @@
-#!/bin/bash
-hostname
-
-#Import cluster properties
-. conf/cluster.properties
-
-#Get the IP address of the cc
-CCHOST_NAME=`cat conf/master`
-CCHOST=`bin/getip.sh`
-
-#Remove the temp dir
-rm -rf $CCTMP_DIR
-mkdir $CCTMP_DIR
-
-#Remove the logs dir
-rm -rf $CCLOGS_DIR
-mkdir $CCLOGS_DIR
-
-#Export JAVA_HOME and JAVA_OPTS
-export JAVA_HOME=$JAVA_HOME
-export JAVA_OPTS=$CCJAVA_OPTS
-
-#Launch hyracks cc script
-chmod -R 755 $HYRACKS_HOME
-$HYRACKS_HOME/hyracks-server/target/appassembler/bin/hyrackscc -client-net-ip-address $CCHOST -cluster-net-ip-address $CCHOST -client-net-port $CC_CLIENTPORT -cluster-net-port $CC_CLUSTERPORT -max-heartbeat-lapse-periods 999999 -default-max-job-attempts 0 -job-history-size 3 &> $CCLOGS_DIR/cc.log &
diff --git a/genomix/genomix-data/target/classes/scripts/startnc.sh b/genomix/genomix-data/target/classes/scripts/startnc.sh
deleted file mode 100644
index 6e0f90e..0000000
--- a/genomix/genomix-data/target/classes/scripts/startnc.sh
+++ /dev/null
@@ -1,49 +0,0 @@
-hostname
-
-MY_NAME=`hostname`
-#Get the IP address of the cc
-CCHOST_NAME=`cat conf/master`
-CURRENT_PATH=`pwd`
-CCHOST=`ssh ${CCHOST_NAME} "cd ${CURRENT_PATH}; bin/getip.sh"`
-
-#Import cluster properties
-. conf/cluster.properties
-
-#Clean up temp dir
-
-rm -rf $NCTMP_DIR
-mkdir $NCTMP_DIR
-
-#Clean up log dir
-rm -rf $NCLOGS_DIR
-mkdir $NCLOGS_DIR
-
-
-#Clean up I/O working dir
-io_dirs=$(echo $IO_DIRS | tr "," "\n")
-for io_dir in $io_dirs
-do
- rm -rf $io_dir
- mkdir $io_dir
-done
-
-#Set JAVA_HOME
-export JAVA_HOME=$JAVA_HOME
-
-IPADDR=`bin/getip.sh`
-#echo $IPADDR
-
-#Get node ID
-NODEID=`hostname | cut -d '.' -f 1`
-
-#Set JAVA_OPTS
-export JAVA_OPTS=$NCJAVA_OPTS
-
-cd $HYRACKS_HOME
-HYRACKS_HOME=`pwd`
-
-#Enter the temp dir
-cd $NCTMP_DIR
-
-#Launch hyracks nc
-$HYRACKS_HOME/hyracks-server/target/appassembler/bin/hyracksnc -cc-host $CCHOST -cc-port $CC_CLUSTERPORT -cluster-net-ip-address $IPADDR -data-ip-address $IPADDR -node-id $NODEID -iodevices "${IO_DIRS}" &> $NCLOGS_DIR/$NODEID.log &
diff --git a/genomix/genomix-data/target/classes/scripts/stopAllNCs.sh b/genomix/genomix-data/target/classes/scripts/stopAllNCs.sh
deleted file mode 100644
index 66ed866..0000000
--- a/genomix/genomix-data/target/classes/scripts/stopAllNCs.sh
+++ /dev/null
@@ -1,6 +0,0 @@
-GENOMIX_PATH=`pwd`
-
-for i in `cat conf/slaves`
-do
- ssh $i "cd ${GENOMIX_PATH}; bin/stopnc.sh"
-done
diff --git a/genomix/genomix-data/target/classes/scripts/stopCluster.sh b/genomix/genomix-data/target/classes/scripts/stopCluster.sh
deleted file mode 100644
index 4889934..0000000
--- a/genomix/genomix-data/target/classes/scripts/stopCluster.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-bin/stopAllNCs.sh
-sleep 2
-bin/stopcc.sh
diff --git a/genomix/genomix-data/target/classes/scripts/stopcc.sh b/genomix/genomix-data/target/classes/scripts/stopcc.sh
deleted file mode 100644
index 1865054..0000000
--- a/genomix/genomix-data/target/classes/scripts/stopcc.sh
+++ /dev/null
@@ -1,10 +0,0 @@
-hostname
-. conf/cluster.properties
-
-#Kill process
-PID=`ps -ef|grep ${USER}|grep java|grep hyracks|awk '{print $2}'`
-echo $PID
-[ "$PID" != "" ] && kill -9 $PID
-
-#Clean up CC temp dir
-rm -rf $CCTMP_DIR/*
diff --git a/genomix/genomix-data/target/classes/scripts/stopnc.sh b/genomix/genomix-data/target/classes/scripts/stopnc.sh
deleted file mode 100644
index 3928bb7..0000000
--- a/genomix/genomix-data/target/classes/scripts/stopnc.sh
+++ /dev/null
@@ -1,23 +0,0 @@
-hostname
-. conf/cluster.properties
-
-#Kill process
-PID=`ps -ef|grep ${USER}|grep java|grep 'Dapp.name=hyracksnc'|awk '{print $2}'`
-
-if [ "$PID" == "" ]; then
- USERID=`id | sed 's/^uid=//;s/(.*$//'`
- PID=`ps -ef|grep ${USERID}|grep java|grep 'Dapp.name=hyracksnc'|awk '{print $2}'`
-fi
-
-echo $PID
-[ "$PID" != "" ] && kill -9 $PID
-
-#Clean up I/O working dir
-io_dirs=$(echo $IO_DIRS | tr "," "\n")
-for io_dir in $io_dirs
-do
- rm -rf $io_dir/*
-done
-
-#Clean up NC temp dir
-rm -rf $NCTMP_DIR/*
diff --git a/genomix/genomix-data/target/test-classes/data/0/text.txt b/genomix/genomix-data/target/test-classes/data/0/text.txt
deleted file mode 100644
index f63a141..0000000
--- a/genomix/genomix-data/target/test-classes/data/0/text.txt
+++ /dev/null
@@ -1,4 +0,0 @@
-@625E1AAXX100810:1:100:10000:10271/1
-AATAGAAG
-+
-EDBDB?BEEEDGGEGGGDGGGA>DG@GGD;GD@DG@F?<B<BFFD?
diff --git a/genomix/genomix-data/target/test-classes/data/webmap/text.txt b/genomix/genomix-data/target/test-classes/data/webmap/text.txt
deleted file mode 100644
index f63a141..0000000
--- a/genomix/genomix-data/target/test-classes/data/webmap/text.txt
+++ /dev/null
@@ -1,4 +0,0 @@
-@625E1AAXX100810:1:100:10000:10271/1
-AATAGAAG
-+
-EDBDB?BEEEDGGEGGGDGGGA>DG@GGD;GD@DG@F?<B<BFFD?
diff --git a/genomix/genomix-data/target/test-classes/edu/uci/ics/genomix/example/kmer/KmerTest.class b/genomix/genomix-data/target/test-classes/edu/uci/ics/genomix/example/kmer/KmerTest.class
deleted file mode 100644
index 69fd8d3..0000000
--- a/genomix/genomix-data/target/test-classes/edu/uci/ics/genomix/example/kmer/KmerTest.class
+++ /dev/null
Binary files differ
diff --git a/genomix/genomix-data/target/test-classes/edu/uci/ics/genomix/example/kmer/KmerUtilTest.class b/genomix/genomix-data/target/test-classes/edu/uci/ics/genomix/example/kmer/KmerUtilTest.class
deleted file mode 100644
index 122107c..0000000
--- a/genomix/genomix-data/target/test-classes/edu/uci/ics/genomix/example/kmer/KmerUtilTest.class
+++ /dev/null
Binary files differ
diff --git a/genomix/genomix-data/target/test-classes/expected/result2 b/genomix/genomix-data/target/test-classes/expected/result2
deleted file mode 100644
index 5e76458..0000000
--- a/genomix/genomix-data/target/test-classes/expected/result2
+++ /dev/null
@@ -1,4 +0,0 @@
-AATAG |A 1
-AGAAG T| 1
-ATAGA A|A 1
-TAGAA A|G 1
diff --git a/genomix/genomix-data/target/test-classes/hadoop/conf/core-site.xml b/genomix/genomix-data/target/test-classes/hadoop/conf/core-site.xml
deleted file mode 100644
index 47dfac5..0000000
--- a/genomix/genomix-data/target/test-classes/hadoop/conf/core-site.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0"?>
-<?xml-stylesheet type="text/xsl" href="configuration.xsl"?>
-
-<!-- Put site-specific property overrides in this file. -->
-
-<configuration>
-
-<property>
- <name>fs.default.name</name>
- <value>hdfs://127.0.0.1:31888</value>
-</property>
-<property>
- <name>hadoop.tmp.dir</name>
- <value>/tmp/hadoop</value>
-</property>
-
-
-</configuration>
diff --git a/genomix/genomix-data/target/test-classes/hadoop/conf/hdfs-site.xml b/genomix/genomix-data/target/test-classes/hadoop/conf/hdfs-site.xml
deleted file mode 100644
index 8d29b1d..0000000
--- a/genomix/genomix-data/target/test-classes/hadoop/conf/hdfs-site.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0"?>
-<?xml-stylesheet type="text/xsl" href="configuration.xsl"?>
-
-<!-- Put site-specific property overrides in this file. -->
-
-<configuration>
-
-<property>
- <name>dfs.replication</name>
- <value>1</value>
-</property>
-
-<property>
- <name>dfs.block.size</name>
- <value>65536</value>
-</property>
-
-</configuration>
diff --git a/genomix/genomix-data/target/test-classes/hadoop/conf/log4j.properties b/genomix/genomix-data/target/test-classes/hadoop/conf/log4j.properties
deleted file mode 100644
index d5e6004..0000000
--- a/genomix/genomix-data/target/test-classes/hadoop/conf/log4j.properties
+++ /dev/null
@@ -1,94 +0,0 @@
-# Define some default values that can be overridden by system properties
-hadoop.root.logger=FATAL,console
-hadoop.log.dir=.
-hadoop.log.file=hadoop.log
-
-# Define the root logger to the system property "hadoop.root.logger".
-log4j.rootLogger=${hadoop.root.logger}, EventCounter
-
-# Logging Threshold
-log4j.threshhold=FATAL
-
-#
-# Daily Rolling File Appender
-#
-
-log4j.appender.DRFA=org.apache.log4j.DailyRollingFileAppender
-log4j.appender.DRFA.File=${hadoop.log.dir}/${hadoop.log.file}
-
-# Rollver at midnight
-log4j.appender.DRFA.DatePattern=.yyyy-MM-dd
-
-# 30-day backup
-#log4j.appender.DRFA.MaxBackupIndex=30
-log4j.appender.DRFA.layout=org.apache.log4j.PatternLayout
-
-# Pattern format: Date LogLevel LoggerName LogMessage
-log4j.appender.DRFA.layout.ConversionPattern=%d{ISO8601} %p %c: %m%n
-# Debugging Pattern format
-#log4j.appender.DRFA.layout.ConversionPattern=%d{ISO8601} %-5p %c{2} (%F:%M(%L)) - %m%n
-
-
-#
-# console
-# Add "console" to rootlogger above if you want to use this
-#
-
-log4j.appender.console=org.apache.log4j.ConsoleAppender
-log4j.appender.console.target=System.err
-log4j.appender.console.layout=org.apache.log4j.PatternLayout
-log4j.appender.console.layout.ConversionPattern=%d{yy/MM/dd HH:mm:ss} %p %c{2}: %m%n
-
-#
-# TaskLog Appender
-#
-
-#Default values
-hadoop.tasklog.taskid=null
-hadoop.tasklog.noKeepSplits=4
-hadoop.tasklog.totalLogFileSize=100
-hadoop.tasklog.purgeLogSplits=true
-hadoop.tasklog.logsRetainHours=12
-
-log4j.appender.TLA=org.apache.hadoop.mapred.TaskLogAppender
-log4j.appender.TLA.taskId=${hadoop.tasklog.taskid}
-log4j.appender.TLA.totalLogFileSize=${hadoop.tasklog.totalLogFileSize}
-
-log4j.appender.TLA.layout=org.apache.log4j.PatternLayout
-log4j.appender.TLA.layout.ConversionPattern=%d{ISO8601} %p %c: %m%n
-
-#
-# Rolling File Appender
-#
-
-#log4j.appender.RFA=org.apache.log4j.RollingFileAppender
-#log4j.appender.RFA.File=${hadoop.log.dir}/${hadoop.log.file}
-
-# Logfile size and and 30-day backups
-#log4j.appender.RFA.MaxFileSize=1MB
-#log4j.appender.RFA.MaxBackupIndex=30
-
-#log4j.appender.RFA.layout=org.apache.log4j.PatternLayout
-#log4j.appender.RFA.layout.ConversionPattern=%d{ISO8601} %-5p %c{2} - %m%n
-#log4j.appender.RFA.layout.ConversionPattern=%d{ISO8601} %-5p %c{2} (%F:%M(%L)) - %m%n
-
-#
-# FSNamesystem Audit logging
-# All audit events are logged at INFO level
-#
-log4j.logger.org.apache.hadoop.fs.FSNamesystem.audit=WARN
-
-# Custom Logging levels
-
-#log4j.logger.org.apache.hadoop.mapred.JobTracker=DEBUG
-#log4j.logger.org.apache.hadoop.mapred.TaskTracker=DEBUG
-#log4j.logger.org.apache.hadoop.fs.FSNamesystem=DEBUG
-
-# Jets3t library
-log4j.logger.org.jets3t.service.impl.rest.httpclient.RestS3Service=ERROR
-
-#
-# Event Counter Appender
-# Sends counts of logging messages at different severity levels to Hadoop Metrics.
-#
-log4j.appender.EventCounter=org.apache.hadoop.metrics.jvm.EventCounter
diff --git a/genomix/genomix-data/target/test-classes/hadoop/conf/mapred-site.xml b/genomix/genomix-data/target/test-classes/hadoop/conf/mapred-site.xml
deleted file mode 100644
index 39b6505..0000000
--- a/genomix/genomix-data/target/test-classes/hadoop/conf/mapred-site.xml
+++ /dev/null
@@ -1,25 +0,0 @@
-<?xml version="1.0"?>
-<?xml-stylesheet type="text/xsl" href="configuration.xsl"?>
-
-<!-- Put site-specific property overrides in this file. -->
-
-<configuration>
-
- <property>
- <name>mapred.job.tracker</name>
- <value>localhost:29007</value>
- </property>
- <property>
- <name>mapred.tasktracker.map.tasks.maximum</name>
- <value>20</value>
- </property>
- <property>
- <name>mapred.tasktracker.reduce.tasks.maximum</name>
- <value>20</value>
- </property>
- <property>
- <name>mapred.max.split.size</name>
- <value>2048</value>
- </property>
-
-</configuration>