This guide introduces UNIX at a very basic level needed for the course
in Biological Sequence Analysis.
If you are already familiar with UNIX you only need to inspect
The exercises will be conducted on Silicon Graphics servers
at CBS, running either IRIX64 (a "flavour" of UNIX) or Altix (a variant
of Linux, which is another "flavour" of UNIX).
The servers will be accessed from portable
Each course participant will get his/her own
You have been assigned user
accounts on the system, each with a home directory. Each internet
student has his/her own account, while on-site students will team up in
pairs, so two students share one account.
The user names are:
stud001, stud002, stud003, ...
Passwords have been distributed to internet
students and will be given to on-site students.
For security reasons, please change your password
after logging in for the first time.
This is done by giving the command yppasswd
- then you will be
asked to enter first your original password, then a new password. A good
password should be at least 6 characters and include both upper-case
letters, lower-case letters and digits.
Unless told otherwise by the exercise teacher, the users
use the server (host)
cell.cbs.dtu.dk, while stud031 and above should use
Logging in to the CBS servers with SSH
Before you log in the first time, you have to make sure that an SSH (Secure Shell) program is available on your computer - see
"Setting up your own computer for
the course" (on-site students won't necessarily need Flash).
Tips for using SSH for Windows
- The copy and paste keyboard shortcuts are different from most
Windows programs: use Ctrl-Insert to copy from the SSH window and
Shift-Insert to paste into it. You can copy the command lines
from the exercise manual in your browser with Ctrl-C and paste
them into the command line with Shift-Insert, if you're lazy
(real bioinformaticans are!).
- Sometimes it is very nice to have more than one shell, e.g. if
you want to
type commands from one shell, while keeping some results in another shell.
On the tool bar (just below the menu bar) there is an icon that looks like
a miniature of the 'SSH Secure Shell' icon. Click on that and you get a new
shell popping up. Very useful.
- You might even want to copy files from the Unix system to your portable.
Next to the minature 'SSH Secure Shell' icon, there is a minature folder icon.
Click on that, and a file transfer window pops up. Just use drag-and-drop
from the desktop to the unix folder (or vice versa).
The window system in the UNIX world (called 'X' or 'X windows') is quite
similar to the PC Windows or Macintosh environments. You will not
encounter an X windows manager during the course, since you are not working
from UNIX terminals, but you can open X windows applications within your
PC Windows interface.
Two things are needed for this to work:
A tunnel that transports X windows communication over a
secure connection (this is handled by SSH), and an X server - see
"Setting up your own computer for
When you start an X windows application from the command line, it is a
good idea to run it in the background by placing an
"&" at the end of the command line:
nedit file &
In this way, the shell will keep running, so that you can continue to
use the command line without closing the nedit
There is a special type of window called 'shell' or 'terminal window'
that is similar to an MS-DOS or "Command Prompt" window in Windows (it
lacks equivalent in the old Macintosh environment, but Mac OS X, being a
UNIX variant, has it). Terminal windows are the principal vehicle of
interaction with a UNIX machine. Their function is to perform the
commands typed into them.
An active terminal window will display a prompt and pause waiting for a
command. The prompt can look like this:
It means that you have logged in to the machine called "genome",
your username is "stud014" and you are in the directory (=folder)
"alignment" in the directory "stud014" in the directory
"people" in the directory "home" at the highest level
of the file hierarchy.
The commands are submitted by typing them after the prompt and then hitting
the RETURN key. They may be copied/pasted from another window (see above).
The command you have typed is not submitted until you hit the RETURN key;
you can move back and forth in the command string using the LEFT and RIGHT
arrow keys and correct mistakes quietly. A command line may be longer
than a line on the screen, just keep typing!
As soon as the RETURN key has been hit the execution starts. Do not be
alarmed if nothing happens at once; sometimes it takes a while to load
and activate a programme.
You can recall the previous command line with the UP arrow key, and then
edit it with LEFT and RIGHT arrow keys and BACKSPACE. Use this to
correct mistakes instead of typing the whole thing again. Note, however,
that you can not use the mouse to position the cursor within the
If you are familiar with MS-DOS, please note these differences in
- Commands and file names are case-sensitive: X.AA and
x.aa are two different files.
- Directories in path names are delimited by / (slash),
not \ (backslash).
- There are no drive letters, such as C:.
- Options to commands are normally preceded with a -
(minus), not a / (slash).
File system navigation
The contents of the current directory (=folder) can be examined by typing
' ("list"). It can look like this:
file1 file2 dir1 dir2
To get more information than just the file names, use 'ls -l
the shorthand 'll
' ("list long"). This gives you the
permissions, ownership, size, and last modification time of all the
You can change to a directory
in the current directory with the command 'cd':
genome[stud014]:/home/people/stud014/alignment> cd dir2
Notice the the prompt changes as you go to another directory.
To go up one level in the hierarchy, use 'cd ..'. To go to
your home directory, use 'cd' with no arguments:
genome[stud014]:/home/people/stud014/alignment/dir2> cd ..
Wherever you are, 'cd
' with no arguments will always take you
to your home directory.
To create a new directory, use 'mkdir newdir'.
Simple file commands
To copy one or more file(s), use cp
cp file newfile
cp file1 file2 etc... directory
To rename a file or move one or more file(s), use mv
mv file newfile
mv file1 file2 etc... directory
To delete (remove) one or more file(s), use rm
rm file1 file2 etc...
See the manual pages
Viewing and editing files
Files containing graphics can be viewed with many different tools. The
choice of tool depends on the format of the file in question,
should be used for postscript files. Most
often it is mentioned in the exercise manual.
Viewing and saving output from commands
Often, a UNIX command will produce much more output than there is
room for on the the screen at one time. In this case, there are two
things you can do:
Most UNIX commands have manual pages
which are viewed with the
The manual page for the command will
automatically be piped to less
is found on the "Using UNIX
There will be staff on duty to assist you in the course of the
exercises. The questions concerning the computer system and the
technicalities of UNIX should be put primarily to the support people:
Hans Henrik Staerfelt, room 011, phone 2471
Peter Wad Sackett, room 020, phone 2427
Kristoffer Rapacki, room 013, phone 2483
The questions concerning the exercise itself should be put to the
teacher responsible for it. The above distinction can be fuzzy so you
should generally grab whoever is at hand and ask for help.