Introduction

GAS is an integrated computer program designed to automate and accelerate the acquisition and analysis of genomic data. It was primarily developed by Alan Young, initially while working at Oxford University.

This is document is the first thing that you should read before attempting to use or install the gas analysis program. After reading this, please see the General Manual for information on how to load, modify and retrieve data using the program, and the Analysis Manual for information on the facilities gas provides for statistically analysing genetic information.

Introduction
Obtaining GAS
Installing GAS
Learning to use GAS
Legal Notice
Help!

Obtaining GAS

For information on the latest version of the gas program, manuals, and example files connect via WWW to

http://users.ox.ac.uk/~ayoung/gas.html

and download the files described below in installing GAS. Versions of gas are currently available for the following systems: IBM-PC DOS, Vax VMS, DEC Ultrix, IBM AIX, DEC Alpha OSF/VMS, SUN Solaris, SGi IRIX and SunOS.

Installing GAS

The full package for gas version 2.3 consists of the following items:

gintro.htm	this introduction file, written in HTML
gmang23.htm	the General Manual, HTML
gmana23.htm	the Analysis Manual, HTML
gfnote23.htm	auxillary Footnotes, HTML
gas	the actual gas program (named `gas.exe` on DOS and VMS systems)

together with a collection of example files. It is recommended that a local copy of the html files is made for normal use. Some of the executable and example files have been compressed into single packages for transfer, and full instructions for restoring them are given below for the supported IBMPC-DOS, unix and VMS operating systems.

IBMPC DOS

The program and all the examples are contained in the file gas23dos.exe, and once you've retrieved this, put it in a local directory and run it (under DOS) by typing

gas23dos

This will extract the whole package of files into your current directory. Note that the gas program runs under DOS rather than Windows, and that the files 32RTM.EXE and DPMI32VM.OVL (which are supplied with the package) must be in the DOS path in order to run gas. Furthermore, the DOS version of gas requires that the WINDOWS directory must also be in the DOS path.

Unix Systems

The executables for different Unix systems are each stored in compressed tar files with names gas23_X.tar.Z where `X' identifies the the platform. The example files are stored in the single file gas23_examples.tar.Z which is common to all Unix platforms *. To extract the program and examples use the command:

zcat filename | tar -xvf -

on all the `tar.Z' files you've retrieved.

VMS

The VMS executable is compiled for the DEC Alpha architecture only. It is stored without any compression or processing - simply download, rename to gas.exe, and run. To use gas from the command line you should rename the gas23.exe file to gas.exe and include the following in your login.com file:

$ gas :== $ [DIRECTORY]gas.exe

where [DIRECTORY] is replaced by the directory (and full disk specification) in which the gas.exe program is placed.

There is no special example package for VMS, so you should load either the DOS or Unix package as described above (the contents of the two are identical).

Learning to use GAS

gas is a large program (about 60,000 lines of code) and most people will use only a small subset of its more advanced features. The best way to get started with it is probably to read the input/output sections of the General Manual then find a real task you're interested in doing and run the relevant example(s) listed in the Analysis or General manuals.

Manual Style

File names and variables are shown in italic font. Keywords and examples input files are shown in teletype font. Note that gas converts all input to lower-case unless it is enclosed in "quotation" marks.

Messages

During operation the gas program may produce four types of message:

status	action taken by gas
INFO	information, note appended to output file
WARNING	possible error, note appended to output file
ERROR	serious error, exit from current gas module
FAILURE	fatal error, immediate exit from program

after gas has completed, a copy of these messages can be found in the logfile (assuming you have requested one with the set logfile command).

If the program terminates with the message INTERNAL ERROR then an internal trap has been triggered and the program will need to be modified and re-compiled to run on your system. In this case please notify Alan Young via email at ayoung@ermine.ox.ac.uk and include the program version, the computer system, the actual input files that were being used when the failure occurred, and the logfile and gas.bug file produced during the run.

Examples

To supplement the manuals there are a series of demonstration examples included as computer files in the distribution package, and it is highly recommended that these are used in conjunction with the text. Output files ending in .ps contain Postscript graphics and must be viewed either on a screen previewer or by sending them to a Postscript compatible printer. If you're learning how to use gas then a good method is to modify the example files to explore how the various optional parameters affect the type of analysis performed.

Legal Notice

The gas program, manuals and associated files are not in the public domain and may not be modified without express permission of the author. However they may be used and copied freely for non-profit-making purposes provided that:

This notice is distributed along with the program.
No charge is made to other parties for services reliant upon gas without express permission from the author.
You agree that neither the author, nor any institution with which he has been associated, accepts any responsibility or liability for either the accuracy of results produced by gas nor for the use to which they are put.
The use of gas is acknowledged in any publications incorporating results produced using the program.

With respect to the clause about acknowledging the use of gas in publications, the following form of words is suggested:

"Data was analysed using the GAS package version2.3, (c) Alan Young, 1993-98."

You should also include any relevant references given in the gas manuals. Note however that the presence of a reference in the manuals does not imply approval of the references' author for the implementation presented in gas, nor conversely is it an endorsement of the method by the author of gas.

Help!

The manuals cover operation of gas only, and are not intended to form a statistics text. References have been included for most of the analytical routines, and these should be consulted for further information on their applicability. Please remember: gas is designed to perform fast accurate analyses of genetic data, but the results will only be useful if an appropriate choice of routines has been made.

The file gasfaq.htm contains answers to some of the commoner questions that users have asked about gas. If you have a query, it is suggested you first post it to the bulletin board bionet.molbio.gene-linkage, and if no suitable response arrives then email: ayoung@ermine.ox.ac.uk

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