1. Welcome to Linux & Shell Scripting Small Group How to learn how to Code Workshop http://onish.web.unc.edu/how-to-learn-how-to-code-linux- small-group/ Erin Osborne Nishimura 1

2. Pop quiz! 2

3. Why should biologists learn to code? Power Efficiency Reproducibility 3

4. What are the barriers to learn to code? Where to begin? This feels awkward Sporadic use Hitting a wall/bug Finding help Cultural barriers 4

5. Where to begin? computing environments and languages Linux – an open-source operating system. bash – A command-writing language. The “language” of linux. Good for tasks, automated workflows, and general management. Python – A general purpose, high-level programming language. Highly readable and writable. Perl – A general purpose, high-level programming language. Great with text files. Javascript – a general purpose, high-level programming language. Specialized for web applications, apps, commonly used in plugins (ImageJ). Ruby -- A very high-level programming language. R – A high level programming language and software environment specialized for statistics and large data management. MATLAB – A computing environment and programming language. Good integration for image analysis. Costs money. MYSQL – Database organization Others? 5 OS PROGRAMMING LANGUAGES MATH-y LANGUAGES DB

6. A HANDS-ON INTRO TO KILLDEVIL How can I use some of these resources? 6

7. Killdevil is a high-performance computing environment Linux operating system 1 login node 774 compute nodes – 48 – 96 GB memory per node. – 12 – 16 CPU’s cores per node. 2 large memory nodes (1 TB) 12 Graphics Processors (GPUs) nodes File systems for storage 7

8. No seriously, what is Killdevil? 8

9. Getting onto Killdevil MAC OS & Linux machines: –Link to killdevil through “Terminal” –Open “Terminal” (in Applications -> Utilities) –Type this: ssh @killdevil.unc.edu -- Add password when prompted PC – Open SSH Secure Shell Client – Click on “Quick Connect” – Hostname = killdevil.unc.edu – Username = – Port Number = 22 – Add password when prompted $ ssh erinosb@killdevil.unc.edu 9

10. WHAT IS LINUX? WHAT IS BASH? 10

11. Linux is a lifestyle Linux is an operating system born out of UNIX Linux comes in many flavors Linux is the most prominent example of the free, open-source movement Linux embodies a philosophy of respect for its users 11

12. bash is the shell for most linux distros 12

13. NAVIGATING THE LINUX ENVIRONMENT 13

14. Getting oriented Commands Manuals Your first two commands: – whoami – Date Learn more about built-in utilities with man $ whoami erinosb $ date Thu Apr 9 13:24:09 EDT 2015 14 $ man whoami

15. Navigating – paths and directories pwd – Print Working Directory cd – Change Directory cd ls – List Contents $ pwd $ cd /nas02/home/ $ ls 15

16. Typical File Structures and Paths 16

17. The Killdevil file structure Directories and sub-directories are “folders” Some important directories on Killdevil http://help.unc.edu/help/getting-started-on- killdevil/#P63_6342 http://help.unc.edu/help/getting-started-on- killdevil/#P63_6342 – ms/ mass storage – netscr/scratch space – ~home directory Making a new directory mkdir Removing a directory rm –ri $ mkdir 01_HTLHTCode $ cd 01_HTLTCode $ ls $ mkdir 01_week1 $ cd 01_week1 $ ls 17

18. Exercise #1 18

19. A few key tips and tricks Naming conventions –NO SPACES! Auto complete with TAB Beginning of code line –CTRL + A End of code line –CTRL + E What if I get stuck? –CTRL+C &#$%! Get me out of here! –Q –CTRL+C –CTRL+D –quit –logout –logoff –logout() –bye –quit() –q() –exit What if I need help? – man – -h – --help – GOOGLE it! – Use language name in search 19

20. Making and Removing files Making a file $ touch Removing a file $ rm –i $ command [-OPTIONS] $ cd $ ls $ cd 01_HTLTCode $ ls $ cd 01_week1 $ ls $ touch 150615_NOTES.txt 20

21. Editing files nano, vi -- OK, but cumbersome –CTRL + X to exit –Type “y” to save SFTP client – better! –Cyberduck, Mozilla –SSH/SFTP Set it up, then drag and drop 21 $ nano 150615_NOTES.txt

22. Getting files onto and off of Kure sftp clients –Cyberduck, Mozilla –SSH/SFTP Set it up, then drag and drop scp scp @killdevil.unc.edu:/path/ sftp, wget 22

23. Copying 23 copying a file $ cp OR $ cp OR $ cp Copying a directory $ cp –r OR $ cp –r

24. moving/renaming Renaming: $ mv Moving: $ mv OR $ mv EXERCISE 3 24

25. Exploring files diff – difference between two files wc – count lines in files * is useful – wild card. Zero, one or more of any character. 25

26. bash Hello World 26

27. Capturing information -- variables $ x=42 $ echo x $ echo $x $ x=“onyen” $ echo $x $ echo ${x} $ echo “$x” $ echo ‘$x’ 27

28. Capturing information -- arrays $ starks= ( “robb” “sansa” “arya” “bran” “rickon” ) $ echo $starks $ echo ${starks} $ echo ${starks[0]} $ echo ${starks[1]} $ echo ${starks[*]} $ starks[1]=“SANSA” $ echo ${starks[1]} 28

29. Don’t use all caps to name variables printenv shows environment variables 29