the cluster version
git-svn-id: https://hyracks.googlecode.com/svn/branches/fullstack_genomix@2957 123451ca-8445-de46-9d55-352943316053
diff --git a/genomix/genomix-hadoop/target/appassembler/bin/maxclique b/genomix/genomix-hadoop/target/appassembler/bin/maxclique
new file mode 100644
index 0000000..5eab8d0
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/bin/maxclique
@@ -0,0 +1,113 @@
+#!/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"/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"/slf4j-jcl-1.6.3.jar:"$REPO"/commons-logging-1.1.1.jar:"$REPO"/slf4j-api-1.6.3.jar:"$REPO"/args4j-2.0.16.jar:"$REPO"/genomix-hadoop-0.2.3-SNAPSHOT.jar
+
+# 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="maxclique" \
+ -Dapp.pid="$$" \
+ -Dapp.repo="$REPO" \
+ -Dapp.home="$BASEDIR" \
+ -Dbasedir="$BASEDIR" \
+ edu.uci.ics.maxclique.Driver \
+ "$@"
diff --git a/genomix/genomix-hadoop/target/appassembler/bin/maxclique.bat b/genomix/genomix-hadoop/target/appassembler/bin/maxclique.bat
new file mode 100644
index 0000000..6a043d0
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/bin/maxclique.bat
@@ -0,0 +1,108 @@
+@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%"\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%"\slf4j-jcl-1.6.3.jar;"%REPO%"\commons-logging-1.1.1.jar;"%REPO%"\slf4j-api-1.6.3.jar;"%REPO%"\args4j-2.0.16.jar;"%REPO%"\genomix-hadoop-0.2.3-SNAPSHOT.jar
+goto endInit
+
+@REM Reaching here means variables are defined and arguments have been captured
+:endInit
+
+%JAVACMD% %JAVA_OPTS% -classpath %CLASSPATH_PREFIX%;%CLASSPATH% -Dapp.name="maxclique" -Dapp.repo="%REPO%" -Dapp.home="%BASEDIR%" -Dbasedir="%BASEDIR%" edu.uci.ics.maxclique.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-hadoop/target/appassembler/lib/ant-1.6.5.jar b/genomix/genomix-hadoop/target/appassembler/lib/ant-1.6.5.jar
new file mode 100644
index 0000000..3beb3b8
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/ant-1.6.5.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/args4j-2.0.16.jar b/genomix/genomix-hadoop/target/appassembler/lib/args4j-2.0.16.jar
new file mode 100644
index 0000000..cfb6a29
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/args4j-2.0.16.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/commons-cli-1.2.jar b/genomix/genomix-hadoop/target/appassembler/lib/commons-cli-1.2.jar
new file mode 100644
index 0000000..ce4b9ff
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/commons-cli-1.2.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/commons-codec-1.3.jar b/genomix/genomix-hadoop/target/appassembler/lib/commons-codec-1.3.jar
new file mode 100644
index 0000000..957b675
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/commons-codec-1.3.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/commons-el-1.0.jar b/genomix/genomix-hadoop/target/appassembler/lib/commons-el-1.0.jar
new file mode 100644
index 0000000..608ed79
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/commons-el-1.0.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/commons-httpclient-3.0.1.jar b/genomix/genomix-hadoop/target/appassembler/lib/commons-httpclient-3.0.1.jar
new file mode 100644
index 0000000..cfc777c
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/commons-httpclient-3.0.1.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/commons-logging-1.1.1.jar b/genomix/genomix-hadoop/target/appassembler/lib/commons-logging-1.1.1.jar
new file mode 100644
index 0000000..1deef14
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/commons-logging-1.1.1.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/commons-net-1.4.1.jar b/genomix/genomix-hadoop/target/appassembler/lib/commons-net-1.4.1.jar
new file mode 100644
index 0000000..9666a92
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/commons-net-1.4.1.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/core-3.1.1.jar b/genomix/genomix-hadoop/target/appassembler/lib/core-3.1.1.jar
new file mode 100644
index 0000000..ae0b635
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/core-3.1.1.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/genomix-hadoop-0.2.3-SNAPSHOT.jar b/genomix/genomix-hadoop/target/appassembler/lib/genomix-hadoop-0.2.3-SNAPSHOT.jar
new file mode 100644
index 0000000..9188416
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/genomix-hadoop-0.2.3-SNAPSHOT.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/hadoop-core-0.20.2.jar b/genomix/genomix-hadoop/target/appassembler/lib/hadoop-core-0.20.2.jar
new file mode 100644
index 0000000..0568eaf
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/hadoop-core-0.20.2.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/hsqldb-1.8.0.10.jar b/genomix/genomix-hadoop/target/appassembler/lib/hsqldb-1.8.0.10.jar
new file mode 100644
index 0000000..e010269
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/hsqldb-1.8.0.10.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/jasper-compiler-5.5.12.jar b/genomix/genomix-hadoop/target/appassembler/lib/jasper-compiler-5.5.12.jar
new file mode 100644
index 0000000..2a410b4
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/jasper-compiler-5.5.12.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/jasper-runtime-5.5.12.jar b/genomix/genomix-hadoop/target/appassembler/lib/jasper-runtime-5.5.12.jar
new file mode 100644
index 0000000..743d906
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/jasper-runtime-5.5.12.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/jets3t-0.7.1.jar b/genomix/genomix-hadoop/target/appassembler/lib/jets3t-0.7.1.jar
new file mode 100644
index 0000000..d87e4d1
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/jets3t-0.7.1.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/jetty-6.1.14.jar b/genomix/genomix-hadoop/target/appassembler/lib/jetty-6.1.14.jar
new file mode 100644
index 0000000..8c503be
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/jetty-6.1.14.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/jetty-util-6.1.14.jar b/genomix/genomix-hadoop/target/appassembler/lib/jetty-util-6.1.14.jar
new file mode 100644
index 0000000..8f924bb
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/jetty-util-6.1.14.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/jsp-2.1-6.1.14.jar b/genomix/genomix-hadoop/target/appassembler/lib/jsp-2.1-6.1.14.jar
new file mode 100644
index 0000000..debfe56
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/jsp-2.1-6.1.14.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/jsp-api-2.1-6.1.14.jar b/genomix/genomix-hadoop/target/appassembler/lib/jsp-api-2.1-6.1.14.jar
new file mode 100644
index 0000000..1be50ab
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/jsp-api-2.1-6.1.14.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/kfs-0.3.jar b/genomix/genomix-hadoop/target/appassembler/lib/kfs-0.3.jar
new file mode 100644
index 0000000..e517c09
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/kfs-0.3.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/oro-2.0.8.jar b/genomix/genomix-hadoop/target/appassembler/lib/oro-2.0.8.jar
new file mode 100644
index 0000000..23488d2
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/oro-2.0.8.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/servlet-api-2.5-6.1.14.jar b/genomix/genomix-hadoop/target/appassembler/lib/servlet-api-2.5-6.1.14.jar
new file mode 100644
index 0000000..6d7404f
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/servlet-api-2.5-6.1.14.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/slf4j-api-1.6.3.jar b/genomix/genomix-hadoop/target/appassembler/lib/slf4j-api-1.6.3.jar
new file mode 100644
index 0000000..08a6c80
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/slf4j-api-1.6.3.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/slf4j-jcl-1.6.3.jar b/genomix/genomix-hadoop/target/appassembler/lib/slf4j-jcl-1.6.3.jar
new file mode 100644
index 0000000..c70e2ce
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/slf4j-jcl-1.6.3.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/xmlenc-0.52.jar b/genomix/genomix-hadoop/target/appassembler/lib/xmlenc-0.52.jar
new file mode 100644
index 0000000..ec568b4
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/xmlenc-0.52.jar
Binary files differ