Introduction to Linux

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Introduction to Linux

• Alan Orth
• April 17, 2010
• ILRI, Nairobi

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What is Linux?
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An Operating System

• (just like Windows and Mac!)
• Created in the 1990s by Linus Torvalds
• Microsoft DOS was too limiting
• UNIX was expensive and restrictive
• Linux was born

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What is Linux?

• Examples of Linux Operating Systems, called
  distributions
• Ubuntu (obvious?)
• Debian
• Fedora
• Redhat
• CentOS
• SuSE
• Big list at http//distrowatch.com

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Why Linux?

• Linux is free
• Free (money)
• Free (freedom... open source)
• Peer reviewed
• makes Linux a good match for science

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Why Linux for Bioinformatics?

• Bioinformatics the application of information
  technology and computer science to the field of
  molecular biology
• Data sets are getting bigger, we need more
  processing power power!
• computers with that kind of power use Linux
• extremely efficient and stable
• excellent in text processing

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Get Your Feet Wet
Most research institutions and universities have
Linux servers.
Use an SSH client like putty to connect to our
Linux server from Windows
Server hpc.ilri.cgiar.org Username
user1 Password user1
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Getting Familiar
Linux has a graphical environment like Windows,
but the real power lies in its command line mode.
In Linux, you type commands in the shell.
After you have entered a command you press Enter
to run the command. Familiarize yourself with
your environment 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
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Getting Familiar
Linux commands come in various forms. Some are
simple, and can be used by themselves whoami c
al Other times you can add arguments to change
the behavior of the command. Arguments are
separated by one or more spaces cal 4
2009 Other other commands require arguments
(they dont make sense to run by themselves)
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Navigating the File System
Files and folders are organized in a hierarchical
fashion. The top of the hierarchy is called the
root. Here is the standard directory structure
in Linux
/
bin etc home
james alan
work pics

• the root directory is often represented by /
• directory is a fancy word for folder

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Navigating the File System
Before we can start solving world hunger, we have
to learn how to move around the file system
comfortably. Analyze your directory structure
using some of the following commands pwd
print the current working directory ls list
the contents of the current directory cd change
to another directory mkdir create a new
directory
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Navigating the File System
Create some directories and get the hang of
moving around them mkdir one mkdir two mkdir
two/three cd one What if you want to move to
two now? There is no two in the current
directory (verify with ls). Our directory
structure looks like this
user1
one
two
You are here
three
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Navigating the File System
If we want to move to the directory two we have
to first move back up in the directory hierarchy.
Once we move back to user1 we will be able to
move into two. cd .. cd two In Linux ..
means parent directory, and you see once we
move to the parent, we're able to then move to
two. Other special directories include . (the
current directory), and (your home directory).
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Working With Files Folders
Commands used for managing files and folders cp
copy a file mv move a file (this is how you
rename) rm delete a file file print the type
of file more read a text file less read a
text file (less is more, but better!) head
print the beginning of a file cat print a file
to the screen
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Working With Files Folders
Reference for some basic commands which use or
require additional arguments ls
-lh (long list of files) ls
-la (long list of hidden files) ls -lh
file (long list of file) mv file
file1 (rename file to file1) cp file
filecopy (copy file to filecopy) rm
file (delete file) rm -i file (delete
file, but ask first) rm -r folder (delete
folder)
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Working With Files Folders
Copy files from Windows ? Linux? Use
WinSCP! SCP is the secure copy protocol which
uses the same username and password you use with
Putty. You can also download files from the
Internet using the following commands wget
web get utility for HTTP and FTP ftp file
transfer protocol links simple, text-based web
browser
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Your First File
Use the text editor nano to create a new file
named hello cd nano hello Type a simple
message and then save the file by writing it to
the disk O (Control-O) In the world of
Linux, the character in key combinations
signifies pressing the Control key. Exit the
text editor by pressing X (Control-X)
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Working With Files Folders
Make a copy of your new text file cp hello
hello2 cat hello more hello Press q when
you're done to quit more. Do you see how the two
are different? cat hello hello2 cat simply
prints a file to the screen, while more is used
to interactively view a text file one page at a
time. Programs like more are called pagers.
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I/O Redirection
By default, command line programs print to
stdout (standard out). I/O redirection
manipulates the input/output of Linux programs,
allowing you to capture it or send it somewhere
else. Make a copy of hello (without using
cp) cat hello gt hello3 cat hello3 The gt
character performs a redirect, taking the
output of the cat command and putting it into the
file hello3.
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I/O Redirection
Now try using echo echo My name is Alan gt
hello3 cat hello3 What happened to hello3?...
It was overwritten! The gt operator creates a
new file to store the output, but if the file
already exists it will be overwritten! Use gtgt
to append to a file echo Appended gtgt hello3
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I/O Redirection
Another useful technique is to redirect one
program's output into another program's input
this is done using a pipe. For example when a
command produces a lot of output, and you want to
read the output one page at a time who
more This is an important technique and will
come in handy when you begin using Linux for text
processing.
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Text Processing Basics
See how many times a certain user is logged in.
grep prints lines which match a given
string who grep aorth wc -l wc counts
words, but can also count lines if you pass it
the -l argument. You can also do the same
thing, using grep's counting argument who
grep -c aorth Count the number of sequences in
a fasta file grep -c gt Tutorial.fna
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More Text Processing
sed, the stream editor, can do powerful things
with text files. One common example is a search
and replace echo Hello echo Hello sed
's/Hello/Goodbye/' Delete blank lines from a
file using sed cat myfile sed //d gt
mynewfile tr can also be used to translate
text echo HELLO tr 'A-Z' 'a-z'
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More Text Processing
But sed is the king of text substitution we can
use something called regular expressions to
match complex text patterns and act on them. In
this example, nucleotides were to be replaced
with integers, A 1, C 2, G 3, T 4 sed
-e 's/\bA\b/1' autosomes.txt less Here we
search for an A bordered by a word barrier on
both sides (standing alone), and replace it with
a 1. Now add a substitution for the C,
etc. Eventually you would want to redirect your
output to a new file instead of less sed -e
's/\bA\b/1' -e 's/\bC\b/2' autosomes.txt gt
autosomes_int.txt
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Shell Scripts
A shell script is a text file with a list of
commands inside. Shell scripts are good for
automating tasks you use often, or running batch
jobs. Enter the following in a new file,
script.sh echo Date and time is date echo
Your current directory is pwd Run the script
like this sh script.sh
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More Shell Scripts
A more advanced shell script utilizing a
loop for num in 1 2 3 do echo We are on
num done
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Where to Get Help
You can always read the manual! To see the man
page for the ls command man ls WWWeb
resources LinuxQuestions.org UbuntuForums.org M
e a.orth_at_cgiar.org