1. Introducing UNIX EMBnet www.embnet.org slide 1 Introducing the UNIX Operating System

2. 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.

3. Introducing UNIX EMBnet www.embnet.org slide 3 X Xprog X · unix> help Press ENTER to 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. users User Interaction Many different users, typically accessing the system from remote machines in different ways

4. 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 permission Have 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.

5. Introducing UNIX EMBnet www.embnet.org slide 5 Connecting to embnet.org Connected. Welcome to the European Molecular Biology Network. Login: Logging in Connect to the unix machine using a suitable program on your local machine. Telnet Xterm Secure Shell Kermit Other 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.

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

7. Introducing UNIX EMBnet www.embnet.org slide 7 The shell or command line 2. Commands username@embnet ~> The shell breaks the command up into individual words ls -ald *.txt The first word is a command ls -ald *.txt The subsequent words form a list of arguments to the command arguments beginning with - are options 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 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. 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 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. Some special characters can lose their special meaning if they are inside quotes. ; Semicolon Seperate commands typed in together.

9. 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.

10. 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 bin usr etc home Several subdirectories under the root directory username Another subdirectory. project seq2seq1seq3seq4 letterprot An 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 /home/username/prot username /home/username/prot prot

11. Introducing UNIX EMBnet www.embnet.org slide 11 Organisation of the file system / binusretchome username project seq2seq1seq3 seq4 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'

12. Introducing UNIX EMBnet www.embnet.org slide 12 Looking at the file system / binusretchome username project seq2seq1seq3 seq4 letterprot ' ls ' lists the files in a directory or directories username@embnet ~> ls protletterproject username@embnet ~> project: seq1seq2seq3seq4 ls project 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.

13. Introducing UNIX EMBnet www.embnet.org slide 13 Moving around the file system / binusretchome username project seq2seq1seq3 seq4 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/project username@embnet ~/project> pwd /home/username/project username@embnet ~> cd project username@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

14. Introducing UNIX EMBnet www.embnet.org slide 14 Changing the file system / binusretchome username project seq2seq1seq3 seq4 letterprot You can create a new subdirectory in the current directory with the command ' mkdir directory ' username@embnet ~> mkdir model model

15. Introducing UNIX EMBnet www.embnet.org slide 15 Changing the file system / binusretchome username project seq2seq1seq3 seq4 letterprot You can delete an empty subdirectory with the command ' rmdir directory ' username@embnet ~> rmdir model model username@embnet ~> model You can delete a file with the command ' rm file ' rm prot username@embnet ~> You can delete a subdirectory and its contents with the command ' rm -rf directory '

16. 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.

17. 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'

18. 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 '

19. 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 ~> letterproject username@embnet ~> More about files: copying files ls cp letter draft username@embnet ~> ls draftletterproject username@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

20. 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. Owner Group World 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. 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 l The file type: - - ordinary file d - directory l - 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

22. 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 letter username@embnet ~> More about files: permissions ls -l letter chmod o-r letter chmod o-r letter For whom you are changing permissions: o - other g - group u - user a - all 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 username@embnet ~> -rwxr----- 1 username users 6048 Aug 17 16:07 letter username@embnet ~> ls -l letter

23. 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.

24. Introducing UNIX EMBnet www.embnet.org slide 24 Useful literature 'Learning the UNIX operating system', O'Reilly press. 'UNIX Quickguide' EMBnet