Unix tutorial-08

Learning Unix/Linux Bioinformatics Orientation 2008 Eric Bishop

Introduction: What is Unix?  An operating system  Developed at AT&T Bell Labs in the 1960’s  Command Line Interpreter  GUIs (Window systems) are now available

Introduction: Unix vs. Linux  Unix was the predecessor of Linux  Linux is a variant of Unix  So is Mac OS X, so much of this tutorial applies to Macs as well  Linux is open source  Most of the machines you’ll use in the Bioinformatics program are running the Linux OS

Introduction: Why Unix/Linux?  Linux is free  It’s fully customizable  It’s stable (i.e. it almost never crashes)  These characteristics make it an ideal OS for programmers and scientists

Connecting to a Unix/Linux system  Open up a terminal:

Connecting to a Unix/Linux system  Open up a terminal: The “prompt” The current directory (“path”) The host

What exactly is a “shell”?  Afterlogging in, Linux/Unix starts another program called the shell  The shell interprets commands the user types and manages their execution  The shell communicates with the internal part of the operating system called the kernel  The most popular shells are: tcsh, csh, korn, and bash  The differences are most times subtle  For this tutorial, we are using bash  Shell commands are CASE SENSITIVE!

Help!  Whenever you need help with a command type “man” and the command name

Unix/Linux File System NOTE: Unix file names are CASE SENSITIVE! /home/mary/ /home/john/portfolio/ The Path

Command: pwd  To find your current path use “pwd”

Command: cd  To change to a specific directory use “cd”

Command: cd  “~” is the location of your home directory

Command: cd  “..” is the location of the directory below current one

Command: ls  To list the files in the current directory use “ls”

Command: ls  ls has many options  -l long list (displays lots of info)  -t sort by modification time  -S sort by size  -h list file sizes in human readable format  -r reverse the order  “man ls” for more options  Options can be combined: “ls -ltr”

Command: ls -ltr  List files by time in reverse order with long listing

General Syntax: *  “*” can be used as a wildcard in unix/linux

Command: mkdir  To create a new directory use “mkdir”

Command: rmdir  Toremove and empty directory use “rmdir”

Creating files in Unix/Linux  Requires the use of an Editor  Various Editors: 1) nano / pico 2) vi 3) emacs

Editing a file using pico or nano  Type “pico” or “nano” at the prompt

Editing a file using pico  To save use “ctrl-x”

Displaying a file  Various ways to display a file in Unix  cat  less  head  tail

Command: cat  Dumps an entire file to standard output  Good for displaying short, simple files

Command: less  “less” displays a file, allowing forward/backward movement within it  return scrolls forward one line, space one page  y scrolls back one line, b one page  use “/” to search for a string  Press q to quit

Command: head  “head” displays the top part of a file  By default it shows the first 10 lines  -n option allows you to change that  “head -n50 file.txt” displays the first 50 lines of file.txt

Command: head  Here’s an example of using “head”:

Command: tail  Same as head, but shows the last lines

File Commands  Copying a file: cp  Move or rename a file: mv  Remove a file: rm

Command: cp  To copy a file use “cp”

Command: mv  To move a file to a different location use “mv”

Command: mv  mv can also be used to rename a file

Command: rm  To remove a file use “rm”

Command: rm  To remove a file “recursively”: rm –r  Used to remove all files and directories  Be very careful, deletions are permanent in Unix/Linux

File permissions  Each file in Unix/Linux has an associated permission level  This allows the user to prevent others from reading/writing/executing their files or directories  Use “ls -l filename” to find the permission level of that file

Permission levels  “r”means “read only” permission  “w” means “write” permission  “x” means “execute” permission  In case of directory, “x” grants permission to list directory contents

File Permissions “The World”

Command: chmod  If you own the file, you can change it’s permissions with “chmod”  Syntax: chmod [user/group/others/all]+[permission] [file(s)]  Below we grant execute permission to all:

Running a program (a.k.a. a job)  Make sure the program has executable permissions  Use “./” to run the program

Running a program: an example  Running the sample perl script “hello_world.pl”

Ending a program  To end a program use “ctrl-c”. To try it:

Command: ps  To view the processes that you’re running:

Command: top  To view the CPU usage of all processes:

Command: kill  To terminate a process use “kill”

Input/Output Redirection (“piping”)  Programs can output to other programs  Called “piping”  “program_a | program_b”  program_a’s output becomes program_b’s input  “program_a > file.txt”  program_a’s output is written to a file called “file.txt”  “program_a < input.txt”  program_a gets its input from a file called “input.txt”

Command: wc  To count the characters, words, and lines in a file use “wc”  The first column in the output is lines, the second is words, and the last is characters

Command: grep  To search files in a directory for a specific string use “grep”

Command: diff  To compare to files for differences use “diff”  Try:diff /dev/null hello.txt  /dev/null is a special address -- it is always empty, and anything moved there is deleted

ssh, scp  ssh is used to securely log in to remote systems, successor to telnet  ssh [username]@[hostname]  Try: ssh yourusername@localhost Type “exit” to log out of session  Scp is used to copy files to/from remote systems, syntax is similar to cp:  scp [local path] [usernme]@[hostname]:[remote file path]  Try:  scp hello.txt yourusername@localhost:scp-test.txt

Unix Web Resources  http://www.ee.surrey.ac.uk/Teaching/Unix/  http://www.ugu.com/sui/ugu/show?help. beginners  http://en.wikipedia.org/wiki/Unix

Unix tutorial-08

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Unix tutorial-08