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I'm trying to set up a part of a site with apache to use shell_exec, while the others have this function restricted though this is my first time so I really have no clue where I'm looking at.

What I need is to call it with a different port (ex. http://localhost:8080, go with other) and practically change the document root, a more "liberal" php.ini to get shell_exec and be able to manage a daemon (to stop/start/restart, manipulate its XML config. )

Although I wonder how it would go in the configuration file, because I still have to maintain the normal sites also with apache and be able to run what I said above.

A: 

This is a pretty broad subject. Maybe this link will help you get started?

http://www.javascriptkit.com/howto/htaccess3.shtml

camomileCase
Sorry, it's not even close to what I want to do. Time to check apache's configuration
allenskd
If you're looking for a web based administration tool for linux you could try webmin which povides shell access, access to the file system, apache configuration stuff and a lot more. http://www.webmin.com/
camomileCase