I have a got a file server and a web server. They are running on physically different machines.
I would like to download a file from the FTP server via JavaScript. T
If by "downloading" you mean "prompt user to save a file from external link" (which basically means open a new window with URL that points to a file) then you can just point user to a script you have control over.
window.open('http://myserver/get_file/filename');
And your server-side get_file script will do all the work of connecting to a FTP and fetching a file