1. Introducing the
UNIX
Operating System

2. What is UNIX? • A family of operating systems • Multitasking
IRIX
SOLARIS
AIX
LINUX
Digital UNIX
MacOSX
...
• Multiuser
Runs more than one program at the same time.
A busy system can be running several hundred or even thousands of programs at the same time.
• Networked
Many different people can use the system at the same time.
It is designed to be linked to other computers and to allow people to work over a network.
The network IS the computer.

3. X What does UNIX do? UNIX Kernel users User Interaction
• Many different users, typically accessing the system from remote machines in different ways
The Shell (or command line)
• Allows the user to interact directly with the computer by typing commands.
• The shell interprets these and instructs the kernel accordingly.
• Very powerful but can be intimidating
• Controls access to the hardware.
• Prevents programs interfering with each other.
• Provides an easy way for programmers to talk to the electronics.
• Controls data storage and protection.
Pointy, clicky program.
• Any number of users can use any number of programs and methods to access the system from any number of remote machines at the same time.
Disk storage
Memory
Network adapter
Modem
Screen
Keyboard
The X Window System
• Graphical interface (point, click, drag, drop etc.)
• Network enabled
• Can use many programs at once
• Is a separate program
• Easier to use than the shell but less powerful
Console programs
• Run from the shell
• Use one program actively at a time
unix> help X
Press ENTER
to continue:
Xprog X
UNIX
Kernel
The Computer

4. Logging in
Unix doesn’t really care where you log in from, though some system administrators might.
You must have a username (login id) to use a unix system
Log in from anywhere you have permission
Have graphical output sent anywhere you have permission
Every user is a member of one or more groups of users.
This identifies you to the system so it can manage your work properly.
This helps the system manage different types of user properly.

5. Logging in
Connect to the unix machine using a suitable program on your local machine.
Connecting to embnet.org
Connected.
Welcome to the European Molecular Biology Network.
Login:
Telnet
Xterm
Secure Shell
Kermit
Other terminal emulators
You may get some messages here from the system administrator.
username
Password:
unix doesn’t show anything on the screen as you type your password.
unix is case sensitive. username is not the same as Username or USERNAME
The system will be unavailable on friday
afternoon for maintenance.
You have new mail.
~>

6. The shell or command line
Several different shells but they behave more or less the same
1. The Prompt.
~>
your present location
your username
the machine you are logged in to
The prompt can be customised to look how you wish

7. The shell or command line
2. Commands
~>
ls -ald *.txt
The subsequent words form a list of arguments to the command
ls -ald *.txt
* is a special character. It means ‘any group of characters’ (including none). The shell finds all the filenames that match anything.txt and adds them to the list of arguments
The first word is a command
ls -ald *.txt
arguments beginning with - are options
ls -ald *.txt
ls -ald *.txt
The shell breaks the command up into individual words
By default the boundary between words is a space.
To get the shell to treat a phrase that includes spaces as a single word, put it in quotes like this:
'my word' or "my word".
Options control how the program runs.
'-a -l -d' is equivalent to '-ald'

8. More Special Characters
Any group of characters including none.
Any single character.
word delineation * ?
" '
Cause the process to run in the background
Pipe.
Pass the output of the command on the left as the input to the command on the right.
Redirect the commands output, eg. to a file
Redirect a commands input. eg. from a file instead of the keyboard.
& |
>
<
Backticks (not ').
Take the output of the command as an argument
String or Dollar
Treat the next word as a variable and write out its value
Backslash.
Change the meaning of the next character.
Semicolon
Seperate commands typed in together. `` $ \ ;
Some special characters can lose their special meaning if they are inside quotes.

9. Organisation "Everything is a file" • An ordinary file contains data.
• A directory contains other files.
• A link is a file that is a shortcut to another file.
The data could be an image, a document, a set of instructions (a program) or any fixed information.
• There are many other types of file .
This is also known as a folder on some systems. A directory can contain other directories (which are then known as sub-directories.)
Files can have more than one name, and be in different directories at the same time
You don't need to worry about these. You probably won't come across one in normal use of the system.

10. Organisation of the file system
/home/username/prot / /
bin
etc
/home/username/prot
home
usr
home
The top of the file system is the directory '/', commonly known as the root directory
/home/username/prot
username
username
Several subdirectories under the root directory
/home/username/prot
prot
project
seq2
seq1
seq3
seq4
letter
prot
Any file in the file system can be uniquely identified by describing the path to it from the root directory.
An example users home directory with a subdirectory and several files
Another subdirectory.

11. Organisation of the file system/
bin
usr
etc
home
username
project
seq2
seq1
seq3
seq4
letter
prot
Organisation of the file system
/home/username
Any process is located somewhere in the filesystem
The command 'pwd' will tell you where.
~>
pwd
'~' is a unix shortcut meaning 'your home directory'

12. Looking at the file system/
bin
usr
etc
home
username
project
seq2
seq1
seq3
seq4
letter
prot
Looking at the file system
'ls' lists the files in a directory or directories
Without an argument, ls lists all the files that don't start with . in the current directory
There are many options to ls that allow you to select and control the information it presents.
~>
~> ls
ls project
prot letter project
project:
seq1 seq2 seq3 seq4

13. Moving around the file system/
bin
usr
etc
home
username
project
seq2
seq1
seq3
seq4
letter
prot
Moving around the file system
/home/username
'..' means the parent directory.
'.' means the current directory. ..
You can move to a different directory with the command 'cd directory '
/home/username/project
/home/username/project
'directory' is the directory to which you want to move. The name can be written as the full path (from root) or as the relative path (from your current directory)
~/project>
~>
repeat using the relative path
~>
~>
cd /home/username/project
cd project
cd ..
~/project>
~>
~/project>
pwd
pwd
pwd

14. Changing the file system/
bin
usr
etc
home
username
project
seq2
seq1
seq3
seq4
letter
prot
Changing the file system
You can create a new subdirectory in the current directory with the command ' mkdir directory '
~>
model
~>
mkdir model

15. Changing the file system/
bin
usr
etc
home
username
project
seq2
seq1
seq3
seq4
letter
prot
Changing the file system
You can delete an empty subdirectory with the command ' rmdir directory '
~>
model
~>
model
You can delete a file with the command ' rm file '
~>
You can delete a subdirectory and its contents with the command
' rm -rf directory '
rmdir model
rm prot

16. More about files: filenames
Filenames can contain any normal text character including spaces and special characters.
Filenames can be almost any length.
It is best to stick to a-z, A-Z, _, -, and numbers.
It is best to keep them short as it saves typing.
If a filename contains a special character or a space you may need to put quotes around the whole path.
Special characters in filenames can cause problems with some programs.

17. More about files: reading files
You can print the contents of one or more files to the screen with the command:
'cat file1 file2 ...'
You can view the contents of one or more files a page at a time on the screen with the command:
' more file1 file2 ...'
cat prints the whole file at once, so a file longer than just a few lines will run off the top of your screen.
You can print the first few lines of a file with the command:
'head file1 file2 ...'
more will let you search through a file, go backwards and forwards and has many other functions.
The last few lines can be viewed with 'tail'

18. More about files: editing files
You can change the content of text files and create new files with a text editor.
Text editors edit text. They do not try to format the text like word processors.
PICO
EMACS
A novice friendly basic text editor used as standard on many systems. Start with the command 'pico filename' VI
A powerful editing environment which can be programmed. It has many modes for auto layout of program code. Start with the command 'emacs filename'
A powerful editor which can be somewhat confusing for newcomers. It is designed for rapid editing of text files and programming. Start with the command 'vi filename'

19. More about files: copying files
You can copy a file with the command
'cp oldfilename newfilename'
If newfilename is a directory, then the file will be copied to 'newfilename/oldfilename'
~> ls
letter project
~>
cp letter draft
~> ls
draft letter project
~>
Warning:
If a file called newfilename already exists then it will be overwritten.
The command 'mv oldfilename newfilename' can be used to rename a file

20. More about files: permissions
• Every file is protected to a greater or lesser extent.
• Permissions determine who can read, write, or execute a given file.
World
Group
Owner
The user who owns the file
Other users in the same group as the user who owns the file.
All the other users in the system.
• Files can have read, write or execute permission for each of the three types of user.

21. More about files: permissions
You can view the permissions for a file by listing it in long format with the command
'ls -l filename'
~>
ls -l letter
Permissions for the owner
-rwxr--r--
Permissions for everyone else
-rwxr--r--
Permissions for the owners group
-rwxr--r--
-rwxr--r-- 1 username users 6048 Aug 17 16:07 letter
Aug 17 16:07
The date the file was last modified
6048
The files size
username
The user who owns the file
users
The files group
The letter l
letter
The files name
The file type:
- - ordinary file
d - directory
l - link (shortcut)

22. More about files: permissions
You can change the permissions for a file with the command
'chmod change filename'
change is the modification you want to make to the files permissions
~>
ls -l letter
-rwxr--r-- 1 username users 6048 Aug 17 16:07 letter
~>
chmod o-r letter
Permissions being changed:
r - read permission
w - write permission
x - execute (run) permission
chmod o-r letter
How you are changing permissions:
- - remove these permissions
+ - add these permissions
= - set permissions to this
chmod o-r letter
For whom you are changing permissions:
o - other
g - group
u - user
a - all
chmod o-r letter
~>
ls -l letter
-rwxr username users 6048 Aug 17 16:07 letter
~>

23. Getting help You can get help on a command by using the command
' man command'
This will bring up the manual page and show it to you screen by screen
If you do not know what a command is called, use the option '-k' to get a list of commands that may be relevant
'man -k word'
This will find all manual pages containing word in the short description of the command.
Try using the options '-h', '-help', or
'--help' if you can't find the man page.

24. Useful literature
'Learning the UNIX operating system', O'Reilly press.
'UNIX Quickguide'
EMBnet
PDF-files provided during this course