UTGB Medaka Setup

• see also Devel/Setup

• SVN repository: ​http://dev.utgenome.org/svn/utgb/trunk/UTGBMedaka
  • This folder contains Eclipse project files, checkout this folder as an Eclipse project

• Server: moonlight.xerial.org
  • ​http://moonlight.xerial.org/GenomeBrowser/GenomeBrowser.html
  • ​http://moonlight.xerial.org/UTGBMedaka/UTGBMedaka.html

Setup the web server (For administrators)

• Install Apache (2.2.x) via RPM
  • sudo chkconfig httpd on
  • sudo service httpd start
• Install ​Tomcat
  • just copied the binary build folder to /home/web/local/tomcat
• Build JK2 (tomcat-apache connector) from source: ​http://tomcat.apache.org/connectors-doc/
  • Install httpd-devel with yum
• JK2 build process

  in jk2-src
  > cd native;
  > ./configure --with-apxs=/usr/sbin/apxs
  > make
  > sudo make install 
  

• JK2 Configuration
  • /etc/httpd/conf.d/workers.property

    worker.list=ajp13
    worker.ajp13.port=8009
    worker.ajp13.host=localhost
    worker.ajp13.type=ajp13
    

  • /etc/httpd/conf.d/tomcat.conf

    LoadModule jk_module modules/mod_jk.so
    
    JkWorkersFile conf.d/workers.properties
    JkLogFile /var/log/httpd/jk.log
    JkLogLevel error
    JkOptions +ForwardKeySize
    
    JkMount /GenomeBrowser ajp13
    JkMount /GenomeBrowser/* ajp13
    #JkMount /* ajp13
    
    JkMount /UTGBMedaka ajp13
    JkMount /UTGBMedaka/* ajp13
    

• Tomcat Startup script (/etc/init.d/tomcat)
  • > sudo chkconfig tomcat on
  • edit JAVA_HOME and CATALINA_HOME environment variables

    #!/bin/sh
    #
    # Startup script for the tomcat
    #
    # chkconfig: 345 80 15
    # description: Tomcat is a Servlet+JSP Engine.
    
    # Source function library.
    . /etc/rc.d/init.d/functions
    
    export JAVA_HOME=/usr/java/jdk
    export CATALINA_HOME=/usr/share/tomcat
    
    envsetup="export JAVA_HOME=$JAVA_HOME; export CATALINA_HOME=$CATALINA_HOME;"
    
    prog=tomcat
    lockfile=/var/lock/subsys/tomcat
    RETVAL=0
    
    start(){
        echo -n $"Starting $prog: "
        daemon --user "tomcat" "$envsetup $CATALINA_HOME/bin/startup.sh"
        RETVAL=$?
        echo
        [ $RETVAL = 0 ] && touch ${lockfile}
        return $RETVAL
    }
    stop() {
        echo -n $"Stopping $prog: "
        daemon --user "tomcat" "$envsetup $CATALINA_HOME/bin/shutdown.sh -force"
        RETVAL=$?
        echo
        [ $RETVAL = 0 ] && rm -f ${lockfile}
    }
    
    
    case "$1" in
     start)
            start
            ;;
     stop)
            stop
            ;;
     restart)
            stop
            start
            ;;
     *)
            echo $"Usage: $prog {start|stop|restart}"
            exit 1
    esac
    
    exit $RETVAL
    

• install ​ANT