From FarmShare

Revision as of 14:17, 8 December 2015

This is intended to be a guide to help you start from zero knowledge of Linux. The same links in a step-by-step guide are here.

While the material may initially seem daunting, don't be discouraged. If you've been able to pick up R or SAS to do any work, you'll be able to easily figure out how to use Linux. However, you do need to dedicate a couple of hours of training time to save you time in the future.

If you find another great tutorial, feel free to edit this page.

Which type of learning do you like:

short interactive tutorial in a browser

interactive crash course (45min):

• http://linuxsurvival.com/

If you can pass all four short quizzes, you can move on.

text html tutorial

intro tutorial (1hr):

• https://cvw.cac.cornell.edu/Linux/default

This is a tutorial that is typical for any specific Linux system, I think this one was originally written for the XSEDE system Stampede at TACC. PDF slides to go along:

• https://portal.tacc.utexas.edu/documents/13601/1080823/LinuxIntro-20141009-eijkhout+%281%29.pdf/bcdcefad-47c5-4741-ab9f-c3380e63df93

You may want to skip the section called "Editing Files", as they show how to do it with the 'vi' program. Instead of 'vi' you should probably start by using 'nano' to edit files, it's easier.

For editing text files, "nano" tutorial here:

• http://www.howtogeek.com/howto/42980/the-beginners-guide-to-nano-the-linux-command-line-text-editor/

longer interactive tutorial in your shell

intro tutorial (4hrs):

• https://swcarpentry.github.io/shell-novice/

This is the first of a series of "software carpentry" tutorials; the equivalent of learning how to use your hammer and measuring tape.

PDF book

self-study book (10hrs):

• http://www.stanford.edu/~chekh/lxes-en-manual-cc.pdf

video tutorial / screencast

Stanford has a contract with lynda.com so all content on Lynda.com is available to us. Check out the course: "Unix for Mac OS X Users". You can skip Chapter 9 which is Mac-specific.

• http://www.lynda.com/Mac-OS-X-10-6-tutorials/Unix-for-Mac-OS-X-Users/78546-2.html

This course covers the same material as the PDF book in the link above, but you get video and narration. It's really pretty good.

Massive Open Online course - MOOC

You may want to take this free self-paced course (40hrs):

• EdX course https://www.edx.org/course/introduction-linux-linuxfoundationx-lfs101x-2

general links

http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001745 "Best Practices for Scientific Computing" a paper written by biologists for biologists in 2014

In support of the basic concepts espoused above, there is a great website:

• https://software-carpentry.org/lessons.html

A great and accessible intro to using 'git' is here:

• http://www-cs-students.stanford.edu/~blynn/gitmagic/

Intro to programming; there are a lot of online resources to learn basic programming, this one is probably a good intro and uses a programming language that is currently popular (9 weeks, 15hrs/week):

• https://www.edx.org/course/introduction-computer-science-mitx-6-00-1x-6#!

The SSDS group has some good Stanford-specific tutorials: https://ssds.stanford.edu/software-resources/getting-started-guides-documents