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The Startup Guide |
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Startup
- To use most of the University's software for bioinformatics you must have a "host"
account on the central computers, particularly the HKUCC system.
- Accounts can be obtained electronically from the
computer centre using the
computer account application
page.
- If you want to use the web interface to GCG, you must apply for a
SeqWeb account
(after you have an HKUCC account).
- After you have obtained an account
- For command line and X-windows programs
- Telnet to HKUCC5 from your PC, Mac or workstation.
- Login to HKUCC5 using your account and password.
- At the command prompt type "bruhkstart" (but not the "") and press the enter key.
- This sets up all the commands for the programs described in this web site.
- For X-windows follow the extra instructions below
- For web based programs use the links from this web site.
Command Line Programs
- Many UNIX programs run through the command line.
- Once you know the commands this can be very fast and efficient. When you start
it may also seem the most difficult.
- At the prompt, enter the command and any switches or parameters.
- The command is the name of the program. See I Want To...,
Software by Group, or
The Software List for the bioinformatics program names.
- Switches are indicators to tell the program what to do.
Usually they are preceded by a "-" (e.g. 'rm -i' see below).
- Parameters are the input and output files and other data that the program will
work on.
- The program documentation, available from the software pages, tells you about
the functions, switches and parameters of the programs.
- The computer centre has a powerpoint tutorial on
Unix basic commands on their
training page.
- Some basic UNIX commands are:
- To run any command, type the command (in italics below) and press the enter key.
- ls ~ to list the files in your current directory (folder).
- ls dirname ~ list the contents of the directory dirname.
- cd dirname ~ to change from the current directory to dirname.
- cd .. ~ change to the directory above this one (the parent directory).
- cd ~ change to your home directory.
- pwd ~ show the current directory you are working in.
- cp fromfile tofile ~ copy fromfile to tofile.
- mv fromfile tofile ~ rename fromfile to tofile.
- rm filename ~ delete filename.
- rm -i filename ~ ask for confirmation before deleting filename.
- more filename ~ display filename on the terminal, bit by bit
(press the space bar to get more or "q" to quit).
- cat filename ~ display filename on the terminal, all at once.
- mkdir dirname ~ create the directory (i.e. new folder) dirname.
- rmdir dirname ~ delete the directory (folder) dirname.
X-windows
- X-windows allows UNIX based computers to have an interface like MicroSoft Windows
PCs and Macs.
- X-windows also lets graphical programs run across a network. By using an "X-server"
on your PC or Mac you can use the windows interface of X-based programs, like
SeqLab, which run on a UNIX machine.
- To run an "X" program on your PC (if it is attached to the network):
- Open the HKUWIN folder on the desktop and double click on the X-cursion icon.
The X-cursion "splash" page will briefly appear and then vanish, leaving an icon
on the task bar.
- Click the run button of the Windows start menu and enter "winipcfg". Note the IP
address shown for the ethernet adapter. If necessary select the
ethernet adapter from the pull-down menu if "PPP adapter" is showing.
- The IP address is of the form "147.8.nn.mm". Note this number.
- Using the telnet program, telnet to HKUCC5 and login using your account name
and password.
- When the command prompt appears enter "setenv DISPLAY 147.8.nn.mm:0". The case
is important! Capital letters for DISPLAY and use the number you
obtained from winipcfg above (substitute the numbers for nn and mm).
- Now you are ready to run X-programs on your PC. Type "bruhkstart" and enter at
the command prompt. Then (for example) type "seqlab" and enter to run the
X-windows interface to GCG.
Last Modified 21/11/01 by
BRUHK support; Copyright © 1999-2001 The University of Hong Kong
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