This looks like a must-read for anyone starting out in computational biology without extensive experience at the command line. The 135-page document linked at the bottom of the Google Group page looks like an excellent primer with lots of examples that could probably be completed in a day or two, and provides a great start for working in a Linux/Unix environment and programming with Perl. This started out as a graduate student course at UC Davis, and is now freely available for anyone who wants to learn Unix and Perl. Also, don't forget about the printable linux command line cheat sheet I posted here long ago.
Google Groups: Unix and Perl for Biologists