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

User (you)

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