How to use PHPStorm/Composer on Windows and then moce project to Ubuntu

I am developing on a Windows machine and the server is a Ubuntu Server. When I move the files to the server the dependencies are not working as they are using windows base files (like exe)

Example: If I do a project using PHP-PhantomJS, ti will download in my bin folder the .exe file. but in reality I would need it to be the one for Ubuntu . Is there a way to make sure it download the correct version when it is put on the server.

Sorry for the question as I have just started to use composer and not sure how to setup PHPStorm correctly.

Thanks