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Linux Introduction: - Dinesh Gupta - ICGEB, India

Linus Torvalds created the Linux operating system in 1991 when he was 21 years old. He was inspired by UNIX but found existing systems like DOS and UNIX too expensive and inadequate. Linux was created using the UNIX-like Minix operating system as a model. Linux is now a free and open source operating system used widely in academia, business, and bioinformatics due to its stability, power, and availability of bioinformatics software.

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0% found this document useful (0 votes)
89 views

Linux Introduction: - Dinesh Gupta - ICGEB, India

Linus Torvalds created the Linux operating system in 1991 when he was 21 years old. He was inspired by UNIX but found existing systems like DOS and UNIX too expensive and inadequate. Linux was created using the UNIX-like Minix operating system as a model. Linux is now a free and open source operating system used widely in academia, business, and bioinformatics due to its stability, power, and availability of bioinformatics software.

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yamuna
Copyright
© © All Rights Reserved
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Download as PPT, PDF, TXT or read online on Scribd
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Linux introduction

• Dinesh Gupta
• ICGEB, India
5/7/2019 11:42 PM
Linux

The Linux operating system (OS) was first


coded by a Finnish computer programmer
called Linus Benedict Torvalds in 1991,
when he was just 21! He had got a new
386, and he found the existing DOS and
UNIX too expensive and inadequate.

In those days, a UNIX-like tiny, free OS called Minix was


extensively used for academic purposes. Since its source code
was available, Linus decided to take Minix as a model.

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Linux directories
• /bin System binaries, including the command shell bin

• /boot Boot-up routines boot


dev
• /dev Device files for all your peripherals
etc
• /etc System configuration files
home
• /home User directories
lib
• /lib Shared libraries and modules lost+found
• /lost+found Lost-cluster files, recovered from a disk-check / misc
• /mnt Mounted file-systems mnt

• /opt Optional software opt


proc
•/proc Kernel-processes pseudo file-system
root
• /root Administrator’s home directory
sbin
• /sbin System administration binaries
tmp
•/usr User-oriented software usr
• /var Various other files: mail, spooling and logging var
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Why use Linux
• A Linux distribution has software worth thousands of dollars, for
virtually no cost
• Linux operating system is reliable, stable, and very powerful
• Linux comes with a complete development environment, including
compilers, toolkits, and scripting languages
• Linux comes with networking facilities, allowing you to share hardware
• Linux utilizes your memory, CPU, and other hardware to the fullest
• A wide variety of commercial software is also available
• Linux is very easily upgradeable
• Supports multiple processors as standard
• True multitasking. So many apps, all at once
• The GUIs
5/7/2019 are
11:42 PM more powerful than Mac!
Why Linux in Bioinformatics ?
• One definition of bioinformatics is "the use of computers to
analyze biological problems.”
• As biological data sets have grown larger and biological
problems have become more complex, the requirements
for computing power have also grown.
• Computers that can provide this power generally use the
Unix operating system - so you must learn Unix
• Linux/UNIX has powerful text processing tools which are
highly suited to working with sequence data
• While many bioinformatics tools have Web interfaces,
many more are available via the UNIX command line

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• Linux/Unix is very stable - computers running
Linux/Unix almost never crash
• Linux/Unix is very efficient
• it gets maximum number crunching power out of your
processor (and multiple processors)
• it can smoothly manage extremely huge amounts of data
• it can give a new life to otherwise obsolete Macs and PCs
• Most new bioinformatics software is created
for Unix - its easy for the programmers

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Few free Bioinformatics SW for
Linux
• Linux operating system, mySYQL database
• Perl - programming language
• Blast and Fasta - similarity search
• Clustal - multiple alignment
• Phylip - phylogenetics
• Phred/Phrap/Consed - sequence assembly
and SNP detection
• EMBOSS - a complete sequence analysis
package created by the EMBL
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Linux Basics
• Freely Downloadable from websites
• Available as sets of CDs
• Installation is very simple
• After installation you can create logins for
different users
• Each user may login by his/her own login
and passwd – own login area
• Upon login, default directory is home
directory of the user
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Linux basics..
• Linux/Unix is case sensitive i.e. WHO is
not same as who
• Unix shell is a command program to
communicate with a computer
• Shell interprets the command that you
enter on keyboards
• Shell commands can be used to automate
various programming tasks
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Linux commands
• Usually short and cryptic like
– vi or rm
• Commands may also have modifiers for
advance options like:
– “ls –l” and “mv –R” are different that “ls” or
“mv” respectively

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Wildcards
• You can substitute the * as a wildcard symbol
for any number of characters in any filename.
• If you type just * after a command, it stands for
all files in the current directory:
lpr * will print all files
• You can mix the * with other characters to form
a search pattern:
ls a*.txt will list all files that start with “a”
and end in “.txt”
• The “?” wildcard stands for any single character:
cp draft?.doc will copy draft1.doc, draft2.doc,
draftb.doc, etc.
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Control characters
• You type Control characters by holding down
the ‘control’ key while also pressing the
specified character.
• While you are typing a command:
• ctrl-W erases the previous word
• ctrl-U erases the whole command line
• Control commands that work (almost) any time
• ctrl-S suspends (halts) output scrolling up on your terminal
screen
• ctrl-Q resumes the display of output on your screen
• ctrl-C will abort any program

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Help on command line
• man : Type man and the name of a
command to read the manual page for that
command. e.g. “man ls”
• apropos: gives a list of commands that
contain a given keyword in their man page
header: e.g. “apropos ls”

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Some important commands in
Linux
• ls, Give a listing of the current directory. Try also ls -l
• cp, Copy file from source to destination
• mv, Move file from source to destination. If both are the same directory,
the file is renamed
• vi, Edit a file. vi is one of the most powerful text editors
•chmod, Change file permissions
•mkdir, rmdir Make/Remove a directory
•cd, Change directory
•rm, Remove a file. Can also remove directory tree
• man ls, Get help for ls. All commands have help

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Networking
• telnet
– Log into a remote host machine.
• rlogin
– Almost the same as telnet, but uses a different protocol.
• ping
– See if a remote host is up.
• ftp
– Transfer files using the File Transfer Protocol.
• netscape
– Run the Netscape web browser.
• trn
– Read Internet News.
• pine
– Read your mail using a full-screen display.
• mail
– Read your mail using an ancient command-line program.
• who
– See who else is logged in.
• talk
– Talk to someone else who is current logged in.
• lp
– Send a file or set of files to a printer.

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Manipulating Files
• cat
– Concatenate program. Can be used to concatenate multiple files together into a single file, or, much more frequently, to send the contents of a file to the terminal
for viewing.
• more
– Scroll through a file page by page. Very useful when viewing large files. Works even with files that are too big to be opened by a text editor.
• less
– A version of more with more features.
• head
– View the head (top) of a file. You can control how many lines to view.
• tail
– View the tail (bottom) of a file. You can control how many lines to view. You can also use tail to view a growing file.
• wc
– Count words, lines and/or characters in one or more files.
• tr
– Substitute one character for another. Also useful for deleting characters.
• sort
– Sort the lines in a file alphabetically or numerically.
• uniq
– Remove duplicated lines in a file.
• cut
– Remove sections from each line of a file or files.
• fold
– Wrap each input line to fit in a specified width.
• grep
– Filter a file for lines matching a specified pattern. Can also be reversed to print out lines that don't match the specified pattern.
• gzip (gunzip)
– Compress (uncompress) a file.
• tar
– Archive or unarchive an entire directory into a single file.
• pico
– Run the pico text editor (good for beginners).
• emacs
– Run the Emacs text editor (good for experts).

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Text Editors Available on Linux
Systems
• vi
– Non-graphical (terminal-based) editor. Guaranteed to be available on any
system. Requires knowledge of arcane keystroke commands. Distinctly
unfriendly to novices.

• emacs
– Window-based editor. Primitive menus make it slightly more friendly to novices.
Still need to know keystroke commands to use. Installed on all Linux distributions
and on most other Unix systems.
• xemacs
– More sophisticated version of emacs, but usually not installed by default. All
common commands are available from menus; however the user interface is still
confusing at first. Very powerful editor, with built-in syntax checking, Web-
browsing, news-reading, manual-page browsing, etc.
• pico
– Simple terminal-based editor available on most versions of Unix. Uses keystroke
commands, but they are listed in logical fashion at bottom of screen.

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Computers in the facility
• Dual boot PCs
• Windows and Linux both
• Logins
– Login: workshop
– Passwd: whotdr05
• You may change your passwd using the
command called “passwd”
• Start practicing !
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