Howdy,
I can't share the exact script due to intellectual property law issues
;)  But it's trivial, basically doing:

export CATALINA_HOME=/foo/bar
$CATALINA_HOME/bin/shutdown.sh
sleep 60
$CATALINA_HOME/bin/startup.sh

That's it.  

>One of the problems I am worried about
>is that Tomcat isn't stopping, so I would need to wait for it to end or
>kill it before I restart it.

If tomcat isn't stopping, find out why and fix it if possible.  The most
typical cause is non-daemon user threads spawned by your apps but never
destroyed properly.  We had that problem and fixed it where we could.
Where we can't, we run only one webapp per instance and have a
ServletContextListener with a System.exit() call in its
contextDestroyed() method to assure shutdown.  Not the cleanest
solution, but it's worked well in practice.

Yoav Shapira
Millennium ChemInformatics

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