I have a JS file that runs via node.js, so normally I crank open a terminal window and type something like node myfile.js and it runs and runs all day; fun.
Assuming you're on Unix-based OS:
You can run shell commands via the exec() function:
// in php file
// to start the script
exec("node myscript.js &", $output);
$output becomes an array of each line of output, so you can see what the process id is. Then you would use that process id to kill the script:
exec("kill " . $processid);
I would avoid any direct interaction with the shell. It would probably be the safest, to solve it this way: