It should be possible to do things like this from any standard unix-terminal:
$ matlab -nodesktop -nosplash -r YOUR-SCRIPT
You might have to doodle around a bit making sure that you get the matlab-path set up to all the directories of the sub-scripts etc. You can have a look at all the command-line options in the /usr/bin/matlab file (or wherever you have it on your system) or simply do:
$ matlab -help
HTH
