Basically, I have a php script that generates a web page, and I would like to send its output to a file (say, index.html).The problem is that php only runs as user nobody, and I can't have chmod ...

It's not hard to create and run a shell script in Linux distros like Ubuntu, but there are a few non-obvious pitfalls you need to avoid. Here's a quick example of how to execute a script in Linux.

If you administer multiple Linux servers, Jack Wallen has an easy script you can use to run commands on all of those servers at once.