For example:
apt-get update
apt-get install mysql-server apache2 php5-mysql apache2-mpm-prefork
Choose your php method:
libapache2-mod-php5 - server-side, HTML-embedded scripting language (Apache 2 module)
libapache2-mod-fcgid - an alternative module compat with mod_fastcgi
libapache2-mod-suphp - Apache2 module to run php scripts with the owner permissions
and install PHP
apt-get install libapache2-mod-php5
This sets up basic software for running a website.
All Linux servers have SSH installed already so you can use an SCP/SFTP program to upload files. On windows WinSCP is recommended at https://winscp.net/eng/index.php
Upload files to /var/www/