You will need to login to your server via ssh and change directory to the project folder using the cd command. From there you will be able to run any command you need to.
You can use the ssh command from within git bash. Your server login details will likely be included in an email sent by your server host when you set up your account. If you are unsure what these are, you can contact your host, and they should be able to retrieve them or change them for you.