I haven't looked on this for a long time so I am not even sure if it works but you can try.

MCRPi

This is a small program that can setup new minecraft server in less than five minutes with boot and shutdown scripts. You can shutdown you raspberry pi with a button but dont worry about that server that is running becose it will shutdown before raspberry pi. That server will automaticaly start running after every boot.

Step by step:

1. Open terminal on your raspberry pi and run these commands:
   sudo apt-get install git
git clone github.com/Verustus/MCRPi
cd MCRPi
chmod +x install.sh
nano configurations.conf
   
2. Now edit the file you are in.
3. After that you need to run ./install.sh and it should setup everything.
4. Now you can just modify file server.properties in your minecraft server folder.

Also if you want to get to the console type sudo screen -ls and then sudo screen -r id(replace the id with the number before the .minecraft)