Introduction to Linux

Dr. George Magklaras

Research Computing Services
By way of Introduction
 By way of Introduction (2)

● Abel supercomputer: Initially number 96 in the Top500 list

● 10000 + cores
● 258 Teraflops/sec max. Theoretical peak performance
● 40 TebiBytes of RAM
● 400 TebiBytes of FhGFS filesystem
 Agenda
● History of Linux
● Why should I choose Linux?
● What is Linux made of (components, choices)
● How you can interact with/use a Linux system?
● The shell and command line interface
● Basic command line skills
 History of Linux

Linus Torvalds Richard Stallman

History of Linux (2)

Courtesy of unix.org
 History of Linux (3)
● UNIX originated as a research project at AT&T Bell Labs in
1969 by Ken Thompson and Dennis Ritchie.
● The first multiuser and multitasking Operating System in the
world.
● Developed in several different versions for various hardware
platforms (Sun Sparc, Power PC, Motorola, HP RISC
Processors).
● In 1991, a student at the University of Helsinki (Linus Torvalds)
created a UNIX-like system to run on the Intel 386 processor.
Intel had already started dominating the PC market, but UNIX
was nearly absent from the initial processor Intel market.
 Why should I choose Linux?
● Best price/performance ratio
● Reliable
● User friendly
● Ubiquitous (from your mobile phone to a
supercomputer)
● Scientific software is developed mostly in Linux
today.
What is Linux made of?
 Linux distributions
● Often referred to as 'distros'.
● The Linux kernel with a set of
programs/applications (text editors, compilers,
office suites, web browsers, etc) that make the
system usable.
● Slackware was one of the first Linux distributions.
● Debian, RedHat (Fedora, RHEL) and Canonical
(Ubuntu) are some of the most popular ones today.
 Linux distributions (2)
● There is a plethora of Linux distros out there,
one of the strongest points of the Linux
community.
● Which one to choose?
● General distributions: to replace your average
desktop/server)
● Function specific distributions: They are tailored
towards a specific audience (i.e. life science)
 Linux distributions (3)
Generic distros:
● Redhat based: Fedora, RHEL, CentOS, Scientific Linux
● Debian based: Debian, Ubuntu
Or task-specific ones (tailored distributions):
● BioLinux
● BioKnoppix
● BioSLAX
● And many others
 Package repositories
● Each Linux distro can connect to one or more
package repositories
● They make it easy to search for/install/uninstall
specific applications
● Package manager (yum, apt)
● “Find me all sequence analysis apps and install
them”
 How to choose a Linux distro
● Try more than one to get a feeling.
● What do your colleagues/team members use?
● Do the package repositories have the applications you
wish to use?
● How long the distro authors will keep maintaining it?
● Do you have a less common laptop/desktop that might
have hardware compatibility problems with that distro?
(rare but it happens)
● http://en.wikipedia.org/wiki/Linux_distribution
 Interacting with Linux
● Using it via a Graphical User Interface (GUI)
(aka Like Windows/Mac, your
smartphone/tablet)
● Using it via the command line (like the
PowerShell on Windows, or your Terminal
window on your Mac)
● Pros and cons in each approach
Linux GUI mode (GNOME)
Linux GUI mode (KDE)
Linux Command Line mode
 So how to install/try Linux?
● Without affecting your current computer setup:
– Use a Live CD (boot your computer from it)
– Do a full installation of Linux on a virtual machine
● Links to distro Live CDs:
– http://fedoraproject.org/wiki/FedoraLiveCD
– http://www.debian.org/CD/live/
● Link to a video (install a Linux OS on Windows using
VirtualBox):
– https://www.youtube.com/watch?v=7jOnscRjaFs
 Basic demo of a Linux system

● Objective: To demonstrate the GUI usage versus

the command line/shell interface (5-10 min)
 The shell and command line
● a powerful and productive tool: manipulates data and
executes several applications under certain
conditions.
● Comes under different flavours, but all of them do the
same thing in slightly different ways.
● Essentially a program itself.
● In this course, we will be concerned with the 'Bash'
shell. Other popular choices are the Tcsh,zsh and
others.
 Basic Shell Principles
● basic syntax for all commands executed at the shell:
command argument1 argument2 argument3...
'command' is the name of the actual shell command you wish to execute.
Every command may take a certain number of arguments (or operands).

Example: cd /storage/mydata

Tip: Always make sure that you have a space between a shell
command and its argument(s).
 Basic Shell Principles (2):
● All UNIX shells are case sensitive with regards to both the
commands and their arguments, in contrast to versions of
Windows/DOS systems. This means that typing:
cd /mydirectory/programs
Is not the same as typing:
CD /MYDIRECTORY/PROGRAMS

Tip: Usually, shell commands are lower case, unless otherwise stated.
 The shell prompt
● The shell prompt is an indication that the system is ready
to execute your commands, but it also gives you useful
info:
georgios@biotin /usr/bin/virexp $

I am user 'georgios' at a server called 'biotin'. I am currently in

a directory called 'virexp' that resides under a directory with
name /usr/bin/. The $ sign says 'you can type now' and it
should have a (sometimes blinking) cursor after it.
 Shell ENVironment and execution
PATH
● a collection of variables collectively known as the “shell
environment” control a number of issues like the
appearance of the shell prompt, what program might be
your default text editor and many other issues.
● One of these variables is the “execution path”: A list of
directories that the shell remembers all the time, in order to
automatically reference certain applications (without you
remembering where they are). Type echo $PATH at the
shell prompt to see this list of directories.
 Filesystem basics
● Ever wondered how the computer keep tracks
of your files?
● Imagine your dossier or file cabinet.
● You label your printed documents and you
organize them in collections.
● Your computer does the same job with your
electronic files using the 'filesystem'.
 Filesystem basics (2)
● Files are named locations on the computer's storage
device. Each filename points to a special filesystem
record that contains information about:
– The type of file (plain data, executable program, special
device)
– The user who created the file
– Access permissions for the file
– The beginning and end of the file record contents in the
filesystem area, as well as its exact position in the
filesystem.
 Filesystem Basics (3)
● Directories (or folders) are containers in which files can be grouped.
● They are arranged in hierarchical mode, starting from the top-level “root”
directory ( / ). The root directory branches into several files and root
subdirectories.
● The consequence of this hierarchy is that each file can be uniquely
identified by a 'path'. A 'path' begins with a / (hint:root directory) and
continues through a list of subdirectories, all the way down to the
filename:
For example: /home/gm/mydata/bac1.seq

Tip: Remember not to confuse the term 'path' with the shell's
execution path, as described in earlier slides.
Directory Hierarchy Diagram
/

bin usr etc home

gm

 /home/gm/mydata/backseq1 mydata
 Navigating the filesystem
● Use 'pwd' to Print your Working Directory. For example, if I
login to the host 'biotin' and I type pwd, I get the following:
georgios@biotin ~ $ pwd
/mn/biotroll/u1/georgios
georgios@biotin ~ $

This means that I am currently in a directory 'georgios', which is

under a directory called 'u1'. This directory itself is under the
'biotroll' directory, which lives under the 'mn' directory. Finally the
mn directory is under the root (toplevel) directory.
 Navigating the filesystem (2)
● Your 'home' directory is the folder you are situated
when you first login to the Linux system shell.
● Usually under /home/username (for example:
/home/georgios)
● Your home directory is also symbolized by ~
● Instead of typing /home/georgios, you could just type ~
Tip: Typing less by using well known symbols
saves you time.
 Navigating the filesystem (3)
● Your instructor says: “Under your home directory, you
will find a directory called “mysequences. Could you
go to that directory and tell me what kind of files exist
under it?”

georgios@biotin ~ $ cd mysequences
georgios@biotin ~/mysequences $
 Navigating the filesystem (4)
● The “cd” command (Change Directory) can be used for moving
around the filesystem. It takes a path as its argument.
● The path can be “absolute”. For example:From your home
directory, you can go to the /usr/bin directory by typing:
georgios@biotin ~ $ cd /usr/bin
georgios@biotin /usr/bin $
● The path can also be “relative”. For example: If you are already
under the /usr directory, you could just type:
georgios@biotin /usr $ cd bin
georgios@biotin /usr/bin $
 Navigating the filesystem (5)
● The command “cd ..” will get you one level up. For example, if we go back
to slide 30 and we assume that you are under the 'mysequences' directory,
if you want to go back to the toplevel of your home directory, you type:
georgios@biotin ~/mysequences $ cd ..
georgios@biotin ~ $
● “..” is a shorthand notation for the previous directory level and it can really
save you from typing long directory names that you cannot remember. It
always works in a relative path context.
● The alternative would be to give an “absolute” path to the cd command:
georgios@biotin ~/mysequences $ cd /mn/biotroll/u1/georgios
georgios@biotin ~ $
 Listing files
● You are back at the mysequences directory under
your home directory. Your instructor asked you to list
the files in the directory:
georgios@biotin ~/mysequences $ ls
seqdocs v2.3_admin.pdf xlrhodop.fasta
georgios@biotin ~/mysequences $

● The ls command lists all the directory contents and is

the equivalent of the dir command in DOS/Windows.
 Listing Files (2)
● The instructor says: “That's not good enough. I want details (file size,
permissions, etc). Why don't you use the -la options of the ls command?”

georgios@biotin ~/mysequences $ ls -la

total 340
drwx------ 3 georgios biotek 62 Mar 26 16:31 .
drwx--x--x 63 georgios biotek 8192 Mar 28 08:45 ..
drwx------ 2 georgios biotek 6 Mar 26 16:31 seqdocs
-rw------- 1 georgios biotek 325479 Mar 26 15:22 v2.3_admin.pdf
-rwxrw---- 1 georgios biotek 1777 Mar 26 15:22 xlrhodop.fasta
 Locating files in the directory tree
● A colleague says: “Help! I have placed a file called
xlrhodop.fast or xlrhodop.fasta (I can't remember the
name) and now I can't find it. Can you help me locate it?”
find [starting point] -name filename -print

'starting point' indicates the directory tree position that we

wish to start searching. 'Filename' could be an
approximation of the file name (it doesn't have to be exact).
 Listing Files (2)
● The instructor says: “That's not good enough. I want details (file size,
permissions, etc). Why don't you use the -la options of the ls command?”

georgios@biotin ~/mysequences $ ls -la

total 340
drwx------ 3 georgios biotek 62 Mar 26 16:31 .
drwx--x--x 63 georgios biotek 8192 Mar 28 08:45 ..
drwx------ 2 georgios biotek 6 Mar 26 16:31 seqdocs
-rw------- 1 georgios biotek 325479 Mar 26 15:22 v2.3_admin.pdf
-rwxrw---- 1 georgios biotek 1777 Mar 26 15:22 xlrhodop.fasta
 Locating filenames in the directory
tree (2)
georgios@biotin ~ $ find ~/ -name xlrhodop.fas*
/mn/biotroll/u1/georgios/xlrhodop.fasta
/mn/biotroll/u1/georgios/mysequences/xlrhodop.fasta

● Note that the wildcard character (*) towards the end of the filename
we are trying to search for. This says that we know that the name
contains the string “xlrhodop.fas”. This would match all relevant
filenames (reporting their exact location in the directory tree)
/mn/biotroll/u1/georgios/xlrhodop.fasta
/mn/biotroll/u1/georgios/mysequences/xlrhodop.fasta
 File permissions (1)
● Every file in UNIX has a set of permission flags that define in a
strict way, who is allowed to read, write (modify) or execute that
file.For example, let's take one of the listed files of the ls -la output
command:

-rwx------ 1 georgios biotek 325479 Mar 26 15:22 v2.3_admin.pdf

Starting from the left, this says: The file xlrhodop.fasta can be read
(r)read, (w)modified,(x)executed by its owner (georgios). Ignore the
rest of the flags for now.
 File permissions (2)
● Directories are no exception to this rule and they also have
permission flags. For example:

drwx------ 2 georgios biotek 6 Mar 26 16:31 seqdocs

● Note the leftmost flag (d). This indicates that 'seqdocs' is a

directory and user georgios has full permissions (read, write
and execute) for that directory. Hence, what we say about
file permissions is true for directory permissions with a few
exceptions (see special file permission consideration slides).
 Changing File Permissions (1)
● Your colleague says “The file v2.3_admin.pdf is quite
important and should not be modified. Can we have it as
read only please? Use the chmod (change mode)
command.”
● The generic syntax for the chmod command is:

chmod [u|g|o (+|-) (r,w,x)] [filename]

DON'T PANIC! We will explain this cryptic syntax with some

examples!
 Changing File Permissions (2):
● The file permissions were:
-rw------- 1 georgios biotek 325479 Mar 26 15:22 v2.3_admin.pdf

Thus, in order to make the file read only we need to

remove the (w) flag. We type at the prompt:
georgios@biotin ~/mysequences $ chmod u-w v2.3_admin.pdf
 Changing File Permissions (3):
●
If we wanted to add back the write permission flag, we would type:
georgios@biotin ~/mysequences $ chmod u+w v2.3_admin.pdf

The + sign says add write permissions (w) for the user (u) that owns
the file.
● You can also add/remove more than one flag at a time:
georgios@biotin ~/mysequences $ chmod u-wx v2.3_admin.pdf

This would remove write (w) and execute permissions (x).

 The execute permission
● The execute permission is important when you
are dealing with programs that you wish to run.
In order to run those programs, you will always
have to set the (x) permission flag
chmod u+x program_name
Tip: Remember this rule, before you try to run a
program in the command line environment.
 The execute permission on
directories
● When changing permissions for directories, you will
need to enable the x flag, in order to allow access to
the directory. Read permission is not enough to allow
access to the directory.

Try: chmod u+rx dir_name

Tip: This is often a confusing concept for beginners.

 Deleting files:
● Given the right permissions, you can remove a file using
the rm command. If, for example, you have a file named
testfile.fasta and you want to remove it, you type:
georgios@biotin ~/mysequences $ rm testfile.fasta

CAUTION: Take great care when you use the rm

command. Whatever you delete, you WILL NOT BE ABLE
TO UNDELETE. There is no “Recycle Bin/Wastebasket” in
command line UNIX.
 Viewing file contents
● Your colleague says: “How do I view the contents of a file? I
want a simple shell command that will show the file contents.”
● The cat command is probably one of the most frequently used
commands. It displays the contents of the file. For example:
cat xlrhodop.fasta
● will display the contents of the file xlrhodop.fasta on the screen
● An alternative way of viewing the file contents is to use a text
editor. We are going to cover the basics of text-editors in the
tutorial later in the course.
 Viewing file contents (2)
● If you use the cat command and you see something
like this:
000731 (Red H▒├ Li┼┤│ 7.2 2.96-
10701.001.001.001.001.001.001.001.001.001.001.001.001.001.01.sy└├▒
b.s├r├▒b.shs├r├▒b.i┼├erp.┼o├e.ABI-├▒±.h▒sh.dy┼sy└.dy┼s├r.±┼┤.┬ersio┼
You are looking at the contents of a binary file which contain
special (non readable) characters. To filter these characters, you
can also use the string command:

Try: strings xlrhodop.fasta

 Viewing file contents (3)
● Your colleague says: “Ohh! I tried to use cat to view a
file but the output is too long for my terminal screen.
The text keeps scrolling and I loose the first lines of
the text. Can I stop this somehow?”
● The less command can actually allow you to view a
file, but it will stop the scrolling of the output, when
your terminal window is filled.
less xlrhodop.fasta
● The more command would do exactly the same thing.
 Viewing File Contents (4)
● Alternatively, if you suspect that the information you want to retrieve is
towards the beginning or the end of the file, you can use head:
head xlrhodop.fasta
This displays the beginning of the file.
● On the other hand, tail can display the end of the file.
tail xlrhodop.fasta
● Both of these commands can be tailored to display a certain number of
lines from the beginning (head) or the end (tail of the file):
head -3 xlrhodop.fasta -> displays the first 3 lines of the file
tail -3 xlrhodop.fasta -> displays the last 3 lines of the file
 Creating Directories
● BB says: “We need a new directory to store all the pdf documents.
Could you create a new directory called pdfdoc under the mysequences
directory?”

georgios@biotin ~/mysequences $ mkdir pdfdoc

georgios@biotin ~/mysequences $ ls -la
drwx------ 4 georgios biotek 75 Mar 28 15:15 .
drwx--x--x 63 georgios biotek 8192 Mar 28 14:53 ..
drwx------ 2 georgios biotek 6 Mar 28 15:15 pdfdoc
drwx------ 2 georgios biotek 6 Mar 26 16:31 seqdocs
-r-------- 1 georgios biotek 325479 Mar 26 15:22 v2.3_admin.pdf
 Removing Directories
“What about the seqdocs directory? Delete it using the rmdir
command”, the instructor replies.
georgios@biotin ~/mysequences $ rmdir seqdocs

So your directory structure should now look like this.

drwx------ 3 georgios biotek 61 Mar 28 15:25 .
drwx--x--x 63 georgios biotek 8192 Mar 28 14:53 ..
drwx------ 2 georgios biotek 6 Mar 28 15:15 pdfdoc
-r-------- 1 georgios biotek 325479 Mar 26 15:22 v2.3_admin.pdf
 Removing Directories (2)
● The 'rmdir' command will promptly remove a directory if
and only if it is empty. If the directory you are trying to
remove (example:pfddoc) contains files, rmdir will fail with
the following error message:
rmdir: `pdfdoc': File exists
You then have to delete all the files under the directory
pdfdoc and then issue the rmdir command.
● The alternative would be to use the rm command.
Remember, directories are 'special' files, so you could
remove them with rm. The next slide shows you how.
 Removing Directories (3)
rm -r -f [directory name]
The -r option says delete directories recursively. The -f option
forces the command to go ahead, despite the fact that the target is
a directory and has files under it. Both options are required. For
example, in order to delete a directory pdfdoc under the
~/mysequences directory, you would type:
rm -r -f pdfdoc/
CAUTION: The usage of 'rm' in this way is even more dangerous,
because it will delete EVERYTHING at a selected directory tree
point, all the way down to the leaf nodes. Always check where you
are with 'pwd' first. If you delete the files, they will be gone forever!
 Copying Files
Your instructor says :”Under the ~/mysequences directory there is a file
called v2.3_admin.pdf . Could you make another copy of that file with the
name 23adminbeta.pdf ?”
You can now use the cp command. The command's general syntax is:
cp [sourcefilepath] [destfilepath]

sourcefilepath:absolute or relative path of the file we want to copy.

destfilepath:absolute or relative path of the new file. This might include

a new filename. If you specify a different directory for the new destination
file and NOT a filename, the source file's name is used by default.
Some examples to illustrate these points follow.
 Copying Files (2)
cp v2.3_admin.pdf 23adminbeta.pdf

As a result, we should now have two files with exactly identical

contents. Note that the size and the permission contents indicate
that the files are identical.
-r-------- 1 georgios biotek 325479 Mar 28 17:01 23adminbeta.pdf
-r-------- 1 georgios biotek 325479 Mar 26 15:22 v2.3_admin.pdf
Also note that 'cp' was executed this time with relative paths for the
source and destination files.
 Copying Files (3)
● ”Could you make a copy of the v2.3_admin.pdf file
into the pdfdoc directory with the name
23adminbeta.pdf“, you could then type:
cp v2.3_admin.pdf perldoc/23adminbeta.pdf

● By default, the 'cp' command preserves the

permissions and ownership rights of files. If in doubt,
use the -p flag. This situation can occur when
performing a copy of the file from computer to
computer using specialist Filesystems such as NFS..
 Copying Directories:
You could copy entire directories recursively
(including any files and their entire subdirectories)
by using the 'cp' command
cp -p -r pdfdoc/ pdfcopy/

The -p flag preserves the permission and ownership

properties and the -r instructs copy to copy all
subdirectories under pdfdoc (recursive copy).
 Moving Files
Sometimes we wish to move the file, in that we wish to copy the file to
a new location without preserving the old one. This is when we can
use the mv command, with the following syntax:
mv sourcefilepath destfilepath

sourcefilepath:absolute or relative path of the file we want to copy.

destfilepath:absolute or relative path of the new file. This might

include a new filename. If you specify a different directory for the new
destination file and NOT a filename, the source file's name is used by
default.
 Moving (or Renaming) Files
mv xlrhodop.fasta myxlr.fasta

This removes the xlrhodop.fasta file and re-generates it with the name
myxlr.fasta, under the same directory.
-r-------- 1 georgios biotek 1777 Mar 26 15:22 myxlr.fasta

'mv' does not only preserve file permissions and ownership rights but it
does also preserve timestamps, so it is an effective way to rename a file.
The UNIX shell has a rename command, but mv could be used
effectively to rename a file.
Tip: All the points we have made about mv for files are also true for
directories.
 Redirecting command output
●
The > symbol is the output redirection operator and can be
used to re-direct the output of any UNIX command that prints
something on the screen.
● Lets suppose that you want to merge two fasta sequences into
a single file:
cat myseq1.fasta myseq2.fasta
would print the contents of both files one-after the other on the
screen (stdout). But what you really want is to place this output to
a file. You can then type:
cat myseq1.fasta myseq2.fasta > mergedseq.fasta
to place the output in the file mergedseq.fasta .
 Redirecting command input
● Suppose that you have a file with numbers and you wish
to sort it from the smaller to the larger number
sort -g < numbers.txt
● Normally, 'sort' would take its input from the keyboard.
However, because you use the input redirection symbol
(<), it is like typing the contents of the file (numbers) in
one step.
● Bottom line: You get your numbers sorted.
● Question: What do you think about this command?
sort -g < numbers.txt > sortednumbers.txt
 The Shell Pipe
● Do you ever wonder how the term 'pipeline' was
established in computing/bioinformatics context?
● One of the most powerful concepts of the
command line environment.
● The more you learn to use it, the more you will
appreciate its power.
● Mastering the shell pipe will allow you to build very
powerful processing utilities to solve your
problems.
The Shell Pipe (2)
 The Shell Pipe (3)
● Quite often, we need to direct the standard output of one
command to the standard input of another.
●
The most commonly used operator to do that is the pipe oparator |
● Suppose for example that we need to count the number of lines of
a text file to see how long it is.
cat mytext.txt | wc -l
The 'cat' command will print all the lines of the file. However, instead
of doing that on the screen, it gives all the output to the 'wc -l'
command. The result is an integer representing the number of lines
of the mytext.txt file.
 References
● UNIX has a built-in reference manual. The
'man' command should be you best friend,
whenever you need help for a particular
command. For example, type
man cat
Every UNIX system should have this facility.
 References (2)
● What if you don't know which command to use?
Let's say for example that I am looking for
pattern matching commands. I would type
apropos pattern
at the shell prompt, and this would give me a list
of relevant commands
 References (3)
● University of Surrey Unix Tutorial for Beginners on the World Wide Web:
http://www.ee.surrey.ac.uk/Teaching/Unix/

● “Developing Bioinformatics Computer Skills”, O'REILLY PRESS, ISBN:

1-56592-664-1, useful for Biologists and Bioinformaticians, especially for
beginners.
http://www.amazon.co.uk/Developing-Bioinformatics-Computer-Skills-Cynt
hia/dp/1565926641

● The EMBnet Unix/Linux Quick Guide:

http://www.embnet.org/sites/default/files/quickguides/guideUNIX.pdf