There are many ways to do what you are needing. I have no idea what "mindcrack.jar" is but typically, it is "craftbukkit.jar" that you run for a server.
I usually setup my CraftBukkit servers to start with on a Windows PC so I use a .bat batch file to startup the server.
Once I'm happy with the server, I then transfer the files to an Ubuntu Server and use .sh scripts to start and manage the server.
Since it needs to run in a terminal so we can type console commands such as "stop" in order to manage it, I use a program called "screen" in my scripts. This allows me to start the server from crontab schedule without ever having to login and I can have other scripts schedule to run that access the console and send it commands such as saving the world to disk, sending messages to users, etc.
I have a rather detailed guide on how I did it in this post.
The command I use to start it is like this:
screen -d -m -S "CraftBukkit" -t "CraftBukkit" java -d64 -Xincgc -Xmx3072 -jar /opt/craftbukkit/craftbukkit.jar nogui