To integrate the OpenEMM 2013 R2 to the installed Tomcat add this
chunk to the server.xml of Tomcat:
TOMCAT_HOME= %%PREFIX%%/apache-tomcat-8.0/lib/

vi TOMCAT_HOME/conf/server.xml

   <Engine>
	.....
	<!-- add this part START -->
	<Host name="OpenEMM"  appBase="webapps-empty" autoDeploy="true" unpackWARs="false" xmlValidation="false" xmlNamespaceAware="false">
		<Alias>localhost</Alias>
		<Valve className="org.apache.catalina.valves.AccessLogValve"
			resolveHosts="false" directory="${catalina.base}/logs/access/" rotatable="true" buffered="true"
			prefix="" suffix="-access_openemm.log" fileDateFormat="yyyyMMdd"
			pattern='%a %l %u %t "%r" %s %b "%{Referer}i" "%{User-Agent}i"' />
		<Context cookies="false" docBase="%%APP_HOME%%/webapps/openemm" path="/openemm" reloadable="true" >
			<JarScanner scanAllDirectories="true" scanBootstrapClassPath="true"/>
		</Context>
		<Context cookies="false" docBase="%%APP_HOME%%/webapps/openemm-ws" path="/openemm-ws2" reloadable="true" />
		<Context docBase="%%APP_HOME%%/webapps/manual" path="/manual" allowLinking="true" />
	</Host>
	<!-- add this part END -->
   </Engine>

Don't forget securing tomcat, or add a httpd in front secured 

# IMPORTANT sendmail is completly controlled from OpenEMM!
# It stops and starts sendmail
# check if sendmail is enabled
sendmail_enable="YES"

# check also if you have a symlink to sendmail
ln -s /etc/rc.d/sendmail /etc/rc.d/

# update the read right on the maillog file
chmod 644 /var/log/maillog

# to keep this change permanent change cron info in /etc/newsyslog.conf
# change line /var/log/maillog                      644  7     *    @T00  JC 

if not change tracking of mail sending / bounces is not working correct

# don't forget to add the link for mysql driver jar to tomcat
ln -s %%PREFIX%%/share/java/classes/mysql-connector-java.jar TOMCAT_HOME/lib
chown -h www TOMCAT_HOME/lib/mysql-connector-java.jar

# setup the database scripts 

in the installed mysql add 2 databases

create database openemm;
create database openemm_cms;

grant the privileges for the 2 db's from where you want to access
grant all privileges on openemm.* to agnitas@'X.Y.%' identified by 'openemm'; 
grant all privileges on openemm_cms.* to agnitas@'X.Y.%' identified by 'openemm';

flush privileges;

# import the inital data
mysql -u root -p openemm < %%PREFIX%%/share/doc/openemm2013/openemm-2013.sql
mysql -u root -p openemm_cms < %%PREFIX%%/share/doc/openemm2013/openemm_cms-2013.sql

#additional config for db acces can be done 
%%PREFIX%%/openemm2013/webapps/openemm/WEB-INF/classes/emm.properties
or
%%PREFIX%%/openemm2013/webapps/openemm/WEB-INF/classes/cms.properties

# startup config for tomcat and OpenEMM
add to /etc/rc.conf
# Tomcat8 Server startup with initial config params for OpenEMM
tomcat8_enable="YES"
tomcat8_java_opts="-server -Djava.awt.headless=true -Xms256m -Xmx512m -XX:MaxPermSize=256m -Xss256k"

# Openemm 2013
openemm2013_enable="YES"

#NOW you are ready to start the tomcat and OpenEMM

service tomcat8 start

service openemm2013 start
or
%%PREFIX%%/etc/rc.d/openemm2013 start