Introduction to Linux operating system. module Basic Bioinformatics PBF

Introduction to Linux operating system

What is Linux?

 A Unix-like Operating System  A famous open source project

 Free to use, distribute, modify under a compatible licence  Produced by a large developer and user community

 A combination of many projects

 Cost of commercial development estimated at USD 7 billion  Companies often make money by selling:

o Support o Training

Linux distributions

Linux FUD

 hard to install, support for different hardware

− _{try recent distribution (eg. Ubuntu)}

 it's ugly

− _{Gnome, KDE, XFCE ... (are they all ugly?)}

 something free can't be good

− _?

 it works different than Windows

What can it do for you?

 Full operating system

 Works well on a variety of hardware, including older hardware  You can adapt it to fit your needs

 Thousands of programs available  Secure by design

 LAMP stack (Linux, Apache, MySQL, PHP)

 Supports a wide range of programming languages  Scalable

GPL licence and source code

 GPL is viral: sharing of changes in GPL

software is requirement to the benefit of community

 When programmers on the Internet can read,

redistribute, and modify the source for a piece of software, it evolves

 People improve it, people adapt it, people fix

bugs. And this can happen at a speed that, compared to conventional software

History

 GNU project started 1984 to produce a Unix-like OS

 Founded by Richard Stallman

 Wrote the GNU manifesto in 1985 outlining philosophy  Software that is free means more than free of charge

"It means that much wasteful duplication of system programming effort will be avoided. This effort can go instead into advancing the state of the art."

 By early 1990s many of the GNU OS utilities were complete

Meanwhile....

Linus Torvalds starts work on the Linux Kernel

 First version released in 1991

 Changes Linux to GPL licence in 1992  Combined with GNU to make an OS

The first “Distros”...

 1992 - MCC Interim Linux

 1992 - Softlanding Linux System (SLS)  1993 - Debian

Linux Today

High profile adoptions:

 French Police

 French Parliament  City of Munich

 Amazon  Google

 Dreamworks (to produce Shrek)

Preinstalled:

 Sub notebooks: EEE & OLPC  £99 laptop

 Dell

 Server hardware

Bioinformatics

 Information technologies used for biology,

BLAST, HMMER, CLUSTALW...

 Lots of data, lots of challenges

 different programming languages  specialized libraries

− _BioPerl − _BioJava − _BioPython

Case Study: SecondLife

Linden Labs uses Linux for SecondLife Servers

 Uses 2000 servers

 Servers located in San Francisco and Dallas  Uses Debian Linux

 CTO: Cory Ondrejka said Debian chosen as

can scale massively with a small number of IT staff

 Each geographic area corresponds to a

processor running software known as a “sim”

Linux on the desktop

 Different desktop systems available  Choose the one you like the best!

Naming Files

 Files are named by

− _{naming each containing}

directory

− _{starting at the root}

 This is known as the

pathname _/etc/conf1

Some Special File Names

 Some file names are special:

− _{/ The root directory (not to be confused with the root user)} − _{. The current directory}

− _{.. The parent (previous) directory} − _{~ My home directory}

 Examples:

− _{./a same as a}

Linux Command Basics

 To execute a command, type its name and

arguments at the command line

ls -l /etc

Command

name Options

(flags)

Command: ls

 List directory contents  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

Redirecting Output

 The output of a command may be sent (piped)

to a file:

ls -l > output

“>” is used to specify the output file

Redirecting Input

 The input of a command may come (be piped)

from a file:

wc < input

“<” is used to specify the input file

General Syntax: *

File Commands

 cp <fromfile> <tofile>

− _{Copy from the <fromfile> to the <tofile>}

 mv <fromfile> <tofile>

− _{Move/rename the <fromfile> to the <tofile>}

 rm <file> Remove the file named <file>

 mkdir <newdir> Make a new directory called

<newdir>

Other commands

 whoami – print the name of the current user  id – print information about the current user

 who – print a list of other users who are logged

in

 date – print the current date and time on the

server

 cal – print a calendar for the current month  echo – print a text string to the screen

Where to Get Help

You can always read the manual! To see the “man page” for the ls command:

Windows console

Download PuTTY

 file: putty.exe

Linux commands

 whoami print effective userid  ls list directory contents

 ls –a

 man ls an interface to the on-line

reference manuals

 whatis ls display simple manual

page descriptions

 pwd print name of current/working

directory