= UTGB Medaka Setup =
 * see also [wiki:Devel/Setup]

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

 * Server: utgenome.org (moonlight.xerial.org CentOS5, which is equivalent to Red Hat Enterprise Linux 5)
   * http://utgenome.org/GenomeBrowser/GenomeBrowser.html
   * http://utgenome.org/UTGBMedaka/UTGBMedaka.html
 
= Setup the web server (For administrators) =
 * Install Java (JDK6)
   * download the rpm
   * set JAVA_HOME variable via /etc/profile.d/java.sh
{{{
# set the java environment
export JAVA_HOME=/usr/java/jdk1.6.0_02
export PATH=$JAVA_HOME/bin:$PATH
}}}
 * Install Apache (2.2.x) via RPM
   * sudo chkconfig httpd on 
   * sudo service httpd start
 * Install [http://tomcat.apache.org/ 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 [http://ant.apache.org ANT] via RPM

= Deployment of the Web Applications =
 * checkout the UTGBMedaka project into /home/web/work/UTGBMedaka
{{{
 /home/web/work> svn checkout http://svn.utgenome.org/utgb/trunk/UTGBMedaka
}}}
 * donwload the GWT library
{{{
 > svn export http://svn.utgenome.org/utgb/trunk/archive/gwt/gwt-linux-1.4.10.tar.gz
 > tar xvfz gwt-linux-1.4.10.tar.gz -C /home/web/local/src
 > ln -s /home/web/local/src/gwt-linux-1.4.10 /home/web/local/gwt
}}}
 * edit the build.properties file
   * set gwt.home, gwt.dev, TOMCAT_HOME, tomcat.manager.username, tomcat.manager.password appropriately
 * Compile & Deploy
{{{
  > cd /home/web/work/UTGBMedaka
  > svn update
  > ant deploy
}}}
 
 * Check the web application
   * http://utgenome.org/UTGBMedaka