I just thought I'd share my experience installing IPT into a Tomcat (5.5 - but experience suggests 6 or 7 wouldn't have helped) installed from Ubuntu packages.

In a nutshell: don't try it!

Ubuntu's packages (and I imagine Debian or any Debian-based system, though I haven't confirmed that) block the normal logging available from the stock Apache versions of Tomcat. What logging there is, gets diverted to the system log (where it is both poorly formatted - no newlines - and truncated). More logging becomes available if you edit 03catalina.policy:

// These permissions apply to JULI
grant codeBase "file:${catalina.home}/bin/tomcat-juli.jar" {
    permission java.security.AllPermission;
};

but in itself that isn't enough to get logging for IPT, and the IPT install fails, but is unable to log the cause of the failure (which I think is the inability to write to the log, but never managed to prove).

The simple solution is to:
- download Tomcat 6 from Apache (http://tomcat.apache.org/download-60.cgi - the tar.gz Binary version), 
- untar it anywhere (I put it in /opt),
- optionally create a symbolic link from /opt/tomcat to the /opt/apache-tomcat* directory you have just created
- stop your existing tomcat ,
- copy all .war files from /var/lib/tomcat*/webapps to the /opt/tomcat/webapps (you may want to copy the subdirectories from there too, if you have applications that store data in them)
- start your new server with /opt/tomcat/bin/startup.sh (setting the environment variable JAVA_OPTS first, with any values that must be passed - for instance, our GeoServer app requires "-D GEOSERVER_DATA_DIR=/opt/geoserver/data")

Don't forget to replace /etc/init.d/tomcat* with an appropriate script to start/stop the new tomcat using /opt/tomcat/bin/startup.sh & shutdown.sh
--
derek broughton
Pointerstop Consulting (for OBIS Canada)