1. Bioinformatics Spring Break Workshop Basic Unix Disclaimer: This set of slides is for educational use only. It contains original content as well as content adapted from a variety of sources including material found on the Web; the copyright symbol, ©, on copyrighted material has been retained.

2. Basic Unix Mark A. Pauley © 2004 - 2011 2 Why Learn Unix?  Many high end-client server systems are Unix based; Unix/Linux skills are much in demand (job skills).  Excellent software-development platform  Much of the software is free (unique culture)  You are an engineer, a mathematician, a scientist, a movie producer: many fields are Unix-centric; i.e., a working knowledge of Unix is required.  Most really exciting Computer Science stuff is done on Unix systems (personal growth).  A good way to learn fundamental computer OS concepts (files, processes, etc.).  A understanding of Unix can  Impress your friends  Make new friends  Destroy and utterly crush your enemies

3. Basic Unix Mark A. Pauley © 2004 - 2011 3 Unix Advantages  It is very popular, so it is easy to find information and get help  Pick up books at the local bookstore  Plenty of helpful websites  Most Computer Science students know Unix  Can run on virtually any computer (IBM, Sun, Compaq, Macintosh,etc)  Free or nearly free  Linux/open source software movement  RedHat, FreeBSD, MKLinux, LinuxPPC, etc.

4. Basic Unix Mark A. Pauley © 2004 - 2011 4 Unix Advantages (cont.)  Very stable – computers running Unix almost never crash  Very efficient  Gets maximum number-crunching power out of your processor (and multiple processors)  Can smoothly manage extremely huge amounts of data  Can give new life to otherwise obsolete Macs and PCs

5. Basic Unix Mark A. Pauley © 2004 - 2011 5 Unix Disadvantages  Unix computers are controlled by a command line interface  Not user-friendly  Steep learning curve; takes a long time to truly master  Hackers love Unix  There are lots of security holes – although probably not as many as Windows ( )  Most computers on the Internet run Unix, so hackers can apply the same tricks to many different computers  Different flavors of Unix have subtle, and sometimes not-so- subtle, differences

6. Basic Unix Mark A. Pauley © 2004 - 2011 6 Unix Help on the Web  Some online Unix tutorials (there are many more):  Unix for Beginners  http://www.ee.surrey.ac.uk/Teaching/Unix/  A basic Unix tutorial (Idaho State University)  http://www.isu.edu/departments/comcom/unix/workshop/unixindex.html  Unix Guru Universe  http://www.ugu.com/sui/ugu/show?help.beginners  Getting Started With The Unix Operating System (Leeds, UK)  http://www.leeds.ac.uk/iss/documentation/beg/beg8/beg8.html

7. Basic Unix Mark A. Pauley © 2004 - 2011 7 General Unix Tips  Unix is case sensitive!!  myfile.txt and MyFile.txt would be different files  ls and LS (if it existed) would be different commands  Every program is independent  The core operating system (known as the kernel) manages each program as a distinct process with its own little chunk of dedicated memory.  If one program runs into trouble, it dies, but does not affect the affect the kernel or the other programs running on the computer.

8. Basic Unix Mark A. Pauley © 2004 - 2011 8 The Unix Shell  You communicate with a Unix computer through a command program known as a shell.  The shell interprets the commands that you type on the keyboard.  There are actually many different shells available for Unix computers, and on some systems you can choose the shell in which you wish to work.  You can use shell commands to write simple programs (scripts) to automate many tasks.

9. Basic Unix Mark A. Pauley © 2004 - 2011 9 Unix Shells  Many shells to choose from...  sh: The Bourne Shell  The original Unix shell  S.R. Bourne designed it at Bell Labs  Not very "user friendly”, but good for programming  sh or a reasonable facsimile comes packaged with virtually every Unix system  csh: The C-shell  A shell whose syntax is more “C”-like  Command history and job control  Make it very popular as a CLI  Comes with most Unix systems

10. Basic Unix Mark A. Pauley © 2004 - 2011 10 Unix Shells (cont.)  tcsh: The T C-Shell  Updated C-shell with better “line-editing”, access to command history, and command and filename completion  bash: The Bourne Again Shell  Aimed at providing a public domain version of the Bourne shell  Default shell for Linux  Implemented as a part of GNU project by public efforts  ksh, zsh, tsh,...

11. Basic Unix Mark A. Pauley © 2004 - 2011 11 Unix Commands - exit and passwd  Unix commands are short and cryptic; e.g., vi, rm.  Computer geeks like it that way; you will get used to it.  Two commands of immediate interest  exit - exit the shell (log off)  passwd - Changes your password (follow the prompts)

12. Basic Unix Mark A. Pauley © 2004 - 2011 12 In-class Practice  Now you try!  Change your password to something different (the system will enforce certain rules).  Exit the system and log back in

13. Basic Unix Mark A. Pauley © 2004 - 2011 13 The Unix Directory Structure  Windows, MacIntosh use the concept of folders.  Unix uses the concept of directories  Both are hierarchical (folders can have subfolders, directories can have sudirectories, etc.)

14. Basic Unix Mark A. Pauley © 2004 - 2011 14 The Unix Directory Structure (cont.)  Directory terminology:  Home directory  Where your files live.  You always go there when you log in.  Working directory  Whatever directory you are currently in.

15. Basic Unix Mark A. Pauley © 2004 - 2011 15 Unix Directory Structure  Different flavors of Unix (including Linux) have a fairly consistent directory structure. root (/) binetcvartmp continentsoceans bats marsupials bandicoot kangaroowombat dev homeusr jack jill opossum wombat

16. Basic Unix Mark A. Pauley © 2004 - 2011 16 Typical Directories  bin : Software for the shell and most common Unix commands.  dev : Short for devices, holds the software necessary to operate peripherals such as printers and terminals.  etc : Contains various administrative files such as lists of user names and passwords.  home : Contains the home directories of users.  tmp : A directory used to hold temporary files.  var : Files that contain information that varies frequently; most commonly, mail directories.

17. Basic Unix Mark A. Pauley © 2004 - 2011 17 Unix Commands - pwd, ls and who  More useful commands:  pwd – Prints the working directory  ls – Lists the contents of the current directory  who – Lists the users currently on the system

18. Basic Unix Mark A. Pauley © 2004 - 2011 18 In-class Practice  Now you try!  Print out your current directory – You should get something like /home/mpauley  List the files in the current directory – Your current directory should appear empty.  Determine who is currently logged into the system. Find your login, and a neighbor’s, in the list.

19. Basic Unix Mark A. Pauley © 2004 - 2011 19 Moving Around  Move around the directory structure using the command cd.  Basic syntax: cd [dir]  dir can be either relative or absolute.  Directory “abbreviations”  ~ Your home directory  Use cd ~ to return to your home directory .. The parent directory; the directory “one up” from the current directory.  Use cd.. to move to the directory “one up” from the current directory. . The current directory  Shortcut  Use cd - to return to the previous directory (where you just were).

20. Basic Unix Mark A. Pauley © 2004 - 2011 20 Creating Directories ( mkdir )  mkdir = (make directory)  Creates a directory.  mkdir [new directory name]  mkdir calendar  Inverse command is rmdir (remove directory) – Directory must be empty.

21. Basic Unix Mark A. Pauley © 2004 - 2011 21 In-class Practice  Now you try!  Navigate to /  Return to your home directory  Navigate to /usr. How many subdirectories are there?  Return to your home directory  Navigate to /usr/local/bin. How many subdirectories are there?  Return to your home directory.  Create a directory called tmp in your home directory  Verify that you created the directory (use ls )  Remove the tmp directory  Verifying that you removed the directory

22. Basic Unix Mark A. Pauley © 2004 - 2011 22 Unix Text Editors  What is a text editor?  Like a word processor but it does not apply formatting styles (bold, italics, different fonts, etc.).  Several text editors installed on hal:  nano – Easy! (the one we’ll start with)  emacs – A heavily-featured editor commonly used in programming  vi/vim – Another heavily-featured editor commonly used in programming  Which text editor is “best” is a holy war. Pick one and get comfortable with it.

23. Basic Unix Mark A. Pauley © 2004 - 2011 23 Unix Text Editors: Design concepts  Editors in Unix come in two general flavors:  Modal editors have “modes”  Generally have input and command modes  Input mode allows entry of text  Command mode allows positioning within the file and more sophisticated text modification  Unix examples: ed and vi  Modeless editors  Have only one mode  Positioning and text manipulation are done by special key sequences (like arrow keys and function keys)  Could also be done by mouse actions or menus  Unix examples: emacs and nano

24. Basic Unix Mark A. Pauley © 2004 - 2011 24 Starting nano  Basic syntax: nano [FILE]  [FILE] can be an existing file.  if [FILE] does not exist, it will be created.  The nano window: commands at the bottom, text area at the top ( ^ stands for the Ctrl key)

25. Basic Unix Mark A. Pauley © 2004 - 2011 25 nano Navigation  Use arrow keys, otherwise:  Ctrl-f : move forward a character.  Ctrl-b : move backward a character.  Ctrl-n : move to the next line.  Ctrl-p : move to the previous line.  Ctrl-v : move forward one page.  Ctrl-y : move backward one page.

26. Basic Unix Mark A. Pauley © 2004 - 2011 26 nano Editing  Inserting  Just type.  Deleting  Ctrl-k : deletes (cuts) the current line of text.  Use Ctrl-k repeatedly until all the lines you want to cut have been deleted (lines are stored in a buffer)  Ctrl-u : uncuts (i.e., pastes) the last cut text.  Pastes all of the lines in the buffer.  Use Ctrl-u repeatedly to simulate copy and paste.  To save your work  Ctrl-o (writeOut)  To exit:  Ctrl-x  If you haven’t yet saved your file, you will be prompted to do so.

27. In-class Practice  Now you try!!  Using the nano text editor, create a file (myInfo.txt) that contains the following information (one per line; start each line with “My name is...”, etc.)  Your name  Your age  The school you go to  What year of school you’re in (freshman, etc.)  The classes you are taking this year/semester/quarter.  Your career goals. Basic Unix Mark A. Pauley © 2004 - 2011 27

28. Basic Unix Mark A. Pauley © 2004 - 2011 28 Command Terminology  Most Unix commands have options and/or arguments – specifies the behavior of the command  Argument  Entered at the end of the command line  Usually a file on which the command will act  cat –n myGene.seq (myGene.seq is the argument)  Options  Entered between the command and its argument  Short options – Generally single letters and prefaced with a single hyphen; may be grouped  Long options – Prefaced with a long hyphen; cannot be grouped.  Case sensitive – In Unix, uppercase and lowercase letters are different.

29. Basic Unix Mark A. Pauley © 2004 - 2011 29 Command Modifiers (cont.)  In the SYNOPSIS section of a man page  [] Optional option/argument  | Options are mutually exclusive ... Option/argument may be repeated  From its man page, ls has a number of possible options and one (optional) argument; nothing is mandatory,

30. Basic Unix Mark A. Pauley © 2004 - 2011 30 Options for ls  Useful options for ls  -a, --all Do not hide entries starting with.  -F --classify Append indicator (one of */=@| ) to entries  -l Use a long listing format  -g Like - l, but do not list owner  [FILE] Information about just a particular file.  Examples:  ls -a List all the files in the current directory  ls -aF or ls -a -F List all the files in the current directory, appending an indicator  ls -al List all the files in the current directory in long format.  ls -al cat.txt List long format information for the file cat.txt

31. Basic Unix Mark A. Pauley © 2004 - 2011 31 Viewing a file (without a editor)  What if you want to view the contents of a file (but not edit it)?  Use the cat command  cat [name of file]  Displays the contents of the entire file (bad for long files)  Use a pager  more [name of file]  Use return key to view the next line of text  Spacebar to read the next page of text  q to quit  / to search.  less [name of file]  Like more but better  Arrow keys to navigate by line  u to move up a page.  A useful option is -N, which numbers the line in the files.

32. Basic Unix Mark A. Pauley © 2004 - 2011 32 In-class practice  Now you try!  Practice using the different option for ls.  Read the man page for cal  What does cal do?  What does the -3 option do?  What does the -m option do?  Display the contents of files in your public_html directory using  cat  less

33. Basic Unix Mark A. Pauley © 2004 - 2011 33 Working with Files: cp  copy (vowels in a command are often omitted)  Copies the contents of one file to another.  cp [file to copy] [new file name]  Flags  -r : will copy directories and all their contents.  Without this flag, the directory will not be copied and you will get an error message.

34. Basic Unix Mark A. Pauley © 2004 - 2011 34 Working with Files: mv  move  Better name could be the rename command.  Changes the name of a file.  mv [old file name] [new file name]  If the two files are in different locations, then the effect is that the file is moved from one directory to another.  Note, if [new file name] is a directory, you will move [old file name] to that directory and keep the original name.

35. Basic Unix Mark A. Pauley © 2004 - 2011 35 Working with Files: rm  remove - Deletes the specified file or files  SYNOPSIS  rm [OPTION]... FILE...  Destructive! The file(s) are gone and cannot be retrieved.  Note: use rm –rf to remove a directory and all of its contents.

36. Basic Unix Mark A. Pauley © 2004 - 2011 36 Working with Files: rmdir  remove (empty) directory  SYNOPSIS rmdir [OPTION]... DIRECTORY...  Deletes a directory (as opposed to the rm command which deletes a file).  The directory must be empty otherwise you will get an error.