Introducing UNIX EMBnet slide 1 Introducing the UNIX Operating System.
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Transcript of Introducing UNIX EMBnet slide 1 Introducing the UNIX Operating System.
Introducing UNIX EMBnet www.embnet.org slide 1
Introducing the
UNIXOperating System
Introducing UNIX EMBnet www.embnet.org slide 2
What is UNIX?
•A family of operating systems
IRIX
SOLARIS
AIX
LINUX
Digital UNIX
HP-UX
...
•Multitasking
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.
•Multiuser
Many different people can use the system at the same time.
•Networked
It is designed to be linked to other computers and to allow people to work over a network.
The network IS the computer.
Introducing UNIX EMBnet www.embnet.org slide 3
XXprogX ·unix> help
Press ENTERto continue:
Disk storage
Memory
Network adapter
Modem
Screen
Keyboard
UNIX
Kernel
What does UNIX do?
The Computer
•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.
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
Console programs•Run from the shell•Use one program actively at a time
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
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.
usersUser Interaction•Many different users, typically accessing the system from remote machines in different ways
Introducing UNIX EMBnet www.embnet.org slide 4
Unix doesn’t really care where you log in from, though some system administrators might.
Logging in
Log in from anywhere you have permissionHave graphical output sent anywhere you have permission
You must have a username (login id) to use a unix system
This identifies you to the system so it can manage your work properly.
Every user is a member of one or more groups of users.
This helps the system manage different types of user properly.
Introducing UNIX EMBnet www.embnet.org slide 5
Connecting to embnet.orgConnected.
Welcome to the European Molecular Biology Network.
Login:
Logging in
Connect to the unix machine using a suitable program on your local machine.
TelnetXtermSecure ShellKermitOther terminal emulators
username
unix is case sensitive. username is not the same as Username or USERNAME
Password:
unix doesn’t show anything on the screen as you type your password.
The system will be unavailable on friday afternoon for maintenance.You have new mail.username@embnet ~>
You may get some messages here from the system administrator.
Introducing UNIX EMBnet www.embnet.org slide 6
The shell or command lineSeveral different shells but they behave more or less the same
username@embnet ~>
your usernamethe machine you are logged in to
your present locationThe prompt can be customised to look how you wish
1. The Prompt.
Introducing UNIX EMBnet www.embnet.org slide 7
The shell or command line2. Commands
username@embnet ~>
The shell breaks the command up into individual words
ls -ald *.txt
The first word is a command
ls -ald *.txtls -ald *.txt
The subsequent words form a list of arguments to the commandarguments beginning with - are options
ls -ald *.txtls -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
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'
Introducing UNIX EMBnet www.embnet.org slide 8
More Special Characters
* ? " '
& | > <
`` $ \
Any group of characters including none. Any single character.word delineation
Cause the process to run in the backgroundPipe.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 fileRedirect a commands input. eg. from a file instead of the keyboard.Backticks (not ').Take the output of the command as an argument
String or DollarTreat the next word as a variable and write out its value
Backslash.Change the meaning of the next character.
Some special characters can lose their special meaning if they are inside quotes.
;SemicolonSeperate commands typed in together.
Introducing UNIX EMBnet www.embnet.org slide 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.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
•There are many other types of file .
You don't need to worry about these. You probably won't come across one in normal use of the system.
Introducing UNIX EMBnet www.embnet.org slide 10
Organisation of the file system
//
The top of the file system is the directory '/', commonly known as the root directory
binbin usr etchome
Several subdirectories under the root directoryusername
Another subdirectory.project
seq2 seq1seq3seq4
letterprotAn example users home directory with a subdirectory and several files
Any file in the file system can be uniquely identified by describing the path to it from the root directory.
/home/username/prot
//
/home/username/prot
home
/home/username/prot
username
/home/username/prot
prot
Introducing UNIX EMBnet www.embnet.org slide 11
Organisation of the file system
//
binbin usr etchome
username
project
seq2 seq1seq3seq4
letterprot
Any process is located somewhere in the filesystem
The command 'pwd' will tell you where.
username@embnet ~> pwd/home/username '~' is a unix shortcut meaning
'your home directory'
Introducing UNIX EMBnet www.embnet.org slide 12
Looking at the file system
//
binbin usr etchome
username
project
seq2 seq1seq3seq4
letterprot
'ls' lists the files in a directory or directories
username@embnet ~> lsprot letter projectusername@embnet ~>project:seq1 seq2 seq3 seq4
ls project
Without an argument, ls lists all the files that don't start with . in the current directoryThere are many options to ls that allow you to select and control the information it presents.
Introducing UNIX EMBnet www.embnet.org slide 13
Moving around the file system
//
binbin usr etchome
username
project
seq2 seq1seq3seq4
letterprot
'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)
You can move to a different directory with the command 'cd directory '
username@embnet ~> cd /home/username/projectusername@embnet ~/project> pwd/home/username/project
username@embnet ~> cd projectusername@embnet ~/project> pwd/home/username/project
username@embnet ~/project> cd ..
'..' means the parent directory.'.' means the current directory.
..
username@embnet ~> pwd/home/username
username@embnet ~>
repeat using the relative path
Introducing UNIX EMBnet www.embnet.org slide 14
Changing the file system
//
binbin usr etchome
username
project
seq2 seq1seq3seq4
letterprot
You can create a new subdirectory in the current directory with the command ' mkdir directory '
username@embnet ~> mkdir modelusername@embnet ~>
model
Introducing UNIX EMBnet www.embnet.org slide 15
Changing the file system
//
binbin usr etchome
username
project
seq2 seq1seq3seq4
letterprot
You can delete an empty subdirectory with the command ' rmdir directory '
username@embnet ~> rmdir model
model
username@embnet ~>
modelYou can delete a file with the command ' rm file '
rm protusername@embnet ~>
You can delete a subdirectory and its contents with the command ' rm -rf directory '
Introducing UNIX EMBnet www.embnet.org slide 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.
Introducing UNIX EMBnet www.embnet.org slide 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 ...'
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 view the contents of one or more files a page at a time on the screen with the command: ' more file1 file2 ...'
more will let you search through a file, go backwards and forwards and has many other functions.
You can print the first few lines of a file with the command: 'head file1 file2 ...'
The last few lines can be viewed with 'tail'
Introducing UNIX EMBnet www.embnet.org slide 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
A novice friendly basic text editor used as standard on many systems. Start with the command 'pico filename'
EMACS
A powerful editing environment which can be programmed. It has many modes for auto layout of program code. Start with the command 'emacs filename'
VI
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'
Introducing UNIX EMBnet www.embnet.org slide 19
If newfilename is a directory, then the file will be copied to 'newfilename/oldfilename'
You can copy a file with the command 'cp oldfilename newfilename'
username@embnet ~>letter projectusername@embnet ~>
More about files: copying files
ls
cp letter draftusername@embnet ~> lsdraft letter projectusername@embnet ~>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
Introducing UNIX EMBnet www.embnet.org slide 20
•Permissions determine who can read, write, or execute a given file.
More about files: permissions
•Every file is protected to a greater or lesser extent.
OwnerGroupWorld
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.
Introducing UNIX EMBnet www.embnet.org slide 21
You can view the permissions for a file by listing it in long format with the command 'ls -l filename'
username@embnet ~> ls -l letter-rwxr--r-- 1 username users 6048 Aug 17 16:07 letter
The letter lThe file type:- - ordinary filed - directoryl - link (shortcut)
Permissions for the owner
-rwxr--r--
Permissions for the owners group
-rwxr--r--
Permissions for everyone else
-rwxr--r-- username
The user who owns the file
users
The files group
6048
The files size
Aug 17 16:07
The date the file was last modified
letter
The files name
More about files: permissions
Introducing UNIX EMBnet www.embnet.org slide 22
change is the modification you want to make to the files permissions
username@embnet ~>
You can change the permissions for a file with the command 'chmod change filename'
-rwxr--r-- 1 username users 6048 Aug 17 16:07 letterusername@embnet ~>
More about files: permissions
ls -l letter
chmod o-r letterchmod o-r letter
For whom you are changing permissions:o - otherg - groupu - usera - all
chmod o-r letter
Permissions being changed:r - read permissionw - write permissionx - execute (run) permission
chmod o-r letter
How you are changing permissions:- - remove these permissions+ - add these permissions= - set permissions to this
username@embnet ~>-rwxr----- 1 username users 6048 Aug 17 16:07 letterusername@embnet ~>
ls -l letter
Introducing UNIX EMBnet www.embnet.org slide 23
You can get help on a command by using the command ' man command'
Getting help
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.
Introducing UNIX EMBnet www.embnet.org slide 24
Useful literature
'Learning the UNIX operating system', O'Reilly press.
'UNIX Quickguide'EMBnet