Permission issues when exporting web project from Eclipse

I have a web application, with the main servlet executing a perl script that does some system work and returns back some string. When I run the application through Eclipse/Tomcat, it works perfectly fine. But when I deploy the application (after exporting the war file) directly through Tomcat, the perl script does nothing. I mean, the script gets called but it can't carry out its system level tasks. I am pretty sure its some policy issue but just can't figure out how and where should I define security policies. Can anyone suggest as to what is the best way of exporting Tomcat application from Eclipse? How do I make sure that the security policy file also gets exported?