So I am sorry if I mess up the names a little. I am still pretty new to linux.
I setup a headless raspberry pi webserver. I installed TightVNC Server on it so I could remote in but for the life of me I can't get the damn server to start when my pi reboots.
My work around to this is to have a php script that I can call from the web that executes a terminal script that starts TightVNC. I don't know if it's called terminal script or not but in windows its called a bat file.
Do php files have this permission? If so what is the php command to execute this file?
To run a shell command with PHP, use shell_exec. It will run as the web user (say, www for Apache), so that user will need to have appropriate permissions. You could, of course, use sudo to get around that - but that is extremely insecure and a very, very bad idea.
So if you had, e.g. a shell script called shellscript.sh sitting on yoru server, and you've written it to do whatever you need it to do, you could run it in php with:
shell_exec('sh path/to/shellscript.sh')
However - I'm not sure I correctly understand what you're trying to do, but it seems to me this is a hacky, very inefficient way to go about things, and it's very likely there is a much smoother solution. Even so, good luck.