Startup Guide

The Startup Guide

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.

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