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Tomcat 5.5.8 and CGI "Write" permissions

Hi,
   I'm trying to run a Perl script in Tomcat 5.5.8, and got Perl successfully configured with the Tomcat application server. However, it does not seem to let the Perl script to write to the hard disk. How do I configure Tomcat to do this? Any help is appreciated!
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Mick Barry
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Will that pose a security risk? The server is running on a machine with enterprise firewall...