1. 1 Applied CyberInfrastructure Concepts ISTA 420/520 Fall 2013 1 Nirav Merchant (nirav@email.arizona.edu) Bio Computing & iPlant Collaborative Eric Lyons (ericlyons@email.arizona.edu) Plant Sciences & iPlant Collaborative University of Arizona http://goo.gl/p4j3mhttp://goo.gl/p4j3m or https://sites.google.com/site/appliedciconcepts/ Will Computers Crash Genomics? Science Vol 331 Feb 2011

2. Tasks for today  Managing your VM  Add user, permission, security considerations etc.  Understanding where the files are  Terminal, editors etc  Shell and scripting  Start building your “Data Science ToolBox”

3. Step #1 for Big Data Toolkit  Command line competency

4. Permissions  Why do you need them ?  What is a ACL (Access Control List) ?  The UNIX model of permissions (next slides are from Greg Wilson at http://software- carpentry.org)http://software- carpentry.org  Path statement and finding things

5. Has unique user name and user ID user

6. Has unique user name and user ID User name is text: "imhotep", "larry", "vlad", … user

7. Has unique user name and user ID User name is text: "imhotep", "larry", "vlad", … User ID is numeric (easier for computer to store)

8. usergroup

9. usergroup Has unique group name and group ID

10. usergroup Has unique group name and group ID User can belongs to zero or more groups

11. usergroup Has unique group name and group ID User can belongs to zero or more groups List is usually stored in /etc/group

12. usergroupall

13. usergroupall Everyone else

14. usergroupall Has user and group IDs

15. usergroupall read

16. usergroupall read write

17. usergroupall read write execute

18. usergroupall read ✔✔✗ write ✔✗✗ execute ✗✗✗

19. usergroupall read ✔✔✗ write ✔✗✗ execute ✗✗✗ File's owner can read and write it

20. usergroupall read ✔✔✗ write ✔✗✗ execute ✗✗✗ File's owner can read and write it Others in group can read

21. usergroupall read ✔✔✗ write ✔✗✗ execute ✗✗✗ File's can read and write it Others in group can read That's all

22. Where are my files ? Understanding layout of data –Home –Root –Tmp Permissions Storage space and planning for it Managing runaway items (more in next class)

23. Security considerations Update your OS (how can you do that ?) Why you should NEVER run as root (how do I add a user ?) Password and keys (and dual factor) Ssh foo

24. What is Shell? Shell is –Command Interpreter that turns text that you type (at the command line) in to actions: –User Interface: take the command from user Programming Shell can do –Customization of a Unix session –Scripting –Many Many automation steps

25. What is Shell? Shell is –Command Interpreter that turns text that you type (at the command line) in to actions: –User Interface: take the command from user Programming Shell can do –Customization of a Unix session –Scripting –Many Many automation steps

26. Customization of a Session Each shell supports some customization. –User prompt –Where to find mail –Shortcuts (alias) The customization takes place in startup files –Startup files are read by the shell when it starts up –The Startup files can differ for different shell

27. Popular Shells  sh Bourne Shell  ksh Korn Shell  csh,tcsh C Shell (for this course)  bash Bourne-Again Shell

28. Flavors of Unix Shells Two main flavors of Unix Shells –Bourne (or Standard Shell): sh, ksh, bash, zsh Fast $ for command prompt –C shell : csh, tcsh better for user customization and scripting %, > for command prompt To check shell: –% echo $SHELL (shell is a pre-defined variable) To switch shell: –% exec shellname (e.g., % exec bash)

29. Startup files and why you should care  bash: /etc/profile (out-of-the-box login shell settings) /etc/bash.bashrc (out-of-box non-login settings) /etc/bash.bashrc.local (global non-login settings) ~/.bash_profile (login shell user customization) ~/.bashrc(non-login shell user customization) ~/.bash_logout (user exits from interactive login shell) http://cli.learncodethehardway.org/bash_cheat_sheet.pdf

30. Some Special Keys How do you invoke tcsh ? Ctrl-U = Delete everything on the command- line Ctrl-A = Move cursor to the front Ctrl-E = Move cursor to the end Ctrl-P = Set the current command-line to the previous command Ctrl-N = Set the current command-line to the next command TAB = Filename completion

31. Preview pieces of toolbox http://datascienceatthecommandline.com/ We will work though Step 5 and go straight to commands

32. Next class  Preparing to play with your data set – Can you download a piece of it ?  Learn about space and process management  Introduction to shell scripting and automation  Start building your Big Data command line tool kit