I'm not sure, and I may be wrong, but it sounds like you may not have sufficient privileges to run arbitrary programs on that server. (Sorry) Try finding out if you can access the server using ssh. If the answer is no, consider getting a server on linode.com, or on nearlyfreespeech.net. They aren't very expensive.
I will ask my friend tomorrow. I have cyberduck and have used it to ssh into my jb iphone before, but alas never a server.
Do you know any site that has a good tutorial for what I will need to do?
You hit 'open connection' make sure ssh is the selected connection type , then input the i.p. address, username & password. http://trac.cyberduck.ch/wiki/help/en
It might be best for you to have your friend guide you through the does and don'ts, given you're not so familiar.
Also reading the Linode library might help you (if your host provider runs Linux): http://library.linode.com/ And although it's specific to their VPS set up and configurations, it's still a Linux machine so you can learn quite a bit.
