This guide introduces UNIX at a very basic level needed for the PhD course
#27803. If you are already familiar with UNIX you only need to inspect
The afternoon exercises will be conducted on the Silicon Graphics servers
at CBS, under IRIX 6.5 (UNIX). The servers will be accessed from portable
computers (IBM ThinkPads), running Windows 2000.
The course participants will groups of two; each group has its own
account on the system. The user names are:
phd03, phd04, phd05, ...
Logging in to the CBS servers: Use SSH as described on programme page
The window system in the UNIX world (called 'X' or 'Xwindows') is quite
similar to the PC Windows or Macintosh environments. Both CYGWIN and the SGI
servers use that system. Windows can be created/deleted, (de)iconized,
scrolled, enlarged, moved etc. with the help of the mouse. Such operations
will not be described here; after a few experiments you will manage to perform
It is possible to copy and paste fragments of text between (most) windows.
Selection (=highlighting) is done with the left mouse button;
pasting in another place with Shift-Insert.
Note: you will also need to copy and paste between CYGWIN
and applications running directly under Windows; in such cases follow the
rules of the system you are in e.g. in Windows copy a text with Ctrl-C
and paste it in CYGWIN with Shift-Insert.
Using the WWW browser
The exercise manuals in this course are linked directly from the course
programme. You should run a WWW browser to view them throughout the exercise.
Start Internet Explorer on your portable under Windows and alternate between
CYGWIN and the browser whenever needed (use Alt-Tab
There is a special type of window called 'shell' or 'terminal window' that
is similar to an MS-DOS window in Windows and
lacks equivalent in the Macintosh environment. 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 "phd14" and you are in the directory (=folder)
"alignment" in the directory "phd14" 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.
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[phd14]:/home/people/phd14/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[phd14]:/home/people/phd14/alignment/dir2> cd ..
Wherever you are, 'cd
' with no arguments will always take you
to your home directory.
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. Most often it is
mentioned in the exercise manual.
Your browser is configured so that it in most cases will launch an
appropriate tool when you view a file (select 'Open file' in the 'File'
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:
The printer is in room 027 (marked with "Printer").
Files can be printed using the 'lp
' command, just type:
lp < filename
where 'filename' is the name of the file you want to print (text file or
postscript graphics file).
Output from a command can be printed directly using a pipe:
command | lp
It is also possible
to print both text files and graphics directly from many Xwindows programs
ghostview and nedit.
Most UNIX commands have manual pages
which are viewed with the
The manual page for the command will
automatically be piped to less
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.