From FarmShare

This is intended to be a guide to help you start from zero knowledge of Linux.

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.

Contents 1 step 0 2 step 1 3 step 2 4 step 3 5 step 4 6 step 5 7 step 6 8 scientific computing

step 0

Zeroth, go through this interactive crash course (45min):

• http://linuxsurvival.com/

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

step 1

First, go through this 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/

step 2

Second, go through this intro tutorial (4hrs):

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

step 3

Third, read through this book (10hrs):

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

step 4

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.

step 5

Fourth, take this free self-paced course (40hrs):

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

step 6

Next, look for a tutorial specific to one of our systems: Farmshare, sherlock, xstream, etc.

scientific computing

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#!