Unix is an operating system commonly used in bioinformatics analysis and programming. Many tools used in bioinformatics work best when run in a Unix-based, command line environment.
This week, you'll learn how to log into a Unix system, navigate the file system, and analyze file contents using Unix commands.
Background and reference materials
The following links are resources Dr. Loraine has reviewed and thinks do a pretty good job of explaining the basics.
Web pages and other docs
- Introduction to UNIX Course Outline http://www.doc.ic.ac.uk/~wjk/UnixIntro/
- Linux File system basics http://www.youtube.com/watch?v=-UeuoG5sAA4&feature=related (We'll watch this in class)
- Software Carpentry - Shell Basics - video tutorials http://showmedo.com/videotutorials/series?name=pQZLHo5Df
To do the assignments, you'll need access to a machine running UNIX. If you do not have access to a computer running UNIX, log into a virtual machine at iPlant.
- Read and do the exercises in Basic UNIX commands - Google Code University http://code.google.com/edu/tools101/linux/basics.html
- Note: Your system may have the nano editor instead of pico. They are very similar, so you can substitute nano if necesssary.
- Read Introduction to the UNIX Operation System and do Tutorials 1 through 8. On tutorial 8, create and edit .bash_profile file instead of .cshrc - we will use the BASH (the Gnu Bourne-Again Shell). See: http://www.ee.surrey.ac.uk/Teaching/Unix/.
- Print a copy of Getting used to Unix, do the exercises, answer the questions.
- Set up your iPlant Atmosphere account and log in via SSH - iPlant setup. Do the exercises and answer the questions.