All files that we used in this class can be downloaded here.
There are many great websites that introduce you how to operate Linux from the command line. Much of the material presented here is taken together from various secondary sources that I encourage to discover by yourself.
The comprehensive Linux course LinuxFoundationX: LFS101x.2 Introduction to Linux offered at edx gives you a great introduction to Linux and then continuous into a deeper level of programming.
Keith Bradnam & Ian Korf offer a great introduction to Unix (and Perl) specifically for biologist on their website.
If you you want to build up general knowledge about computer programming, I recommend the highly informative as well as entertaining CS50 seminar by David J. Malan.
Useful resources for git:
Git - Primary Git SCM website.
Try Git - Code School - More interactive practice with Git.
Free Git Pro Book - Great free in-depth book about Git.
Github.com - Free collaborative web-based portal for Git.
Bitbucket.org - Free collaborative web-based protal for Git.
More help for programming with Python:
Python Practice Book - Comprehensive Python Manual.
Python data types - Guide through all Python data types.