Hallo,
At the 'Genes, Proteins and Computers' conference at Chester a lot of
interest was expressed in the version of the GCG package that we are
running on SUN4 UNIX machines. We therefore thought it might be useful
describe the situation in more detail to the general community.
History:
In June 1988 two institutes of the UK Medical Research Council, the
Clinical Research Centre at Harrow, Middx (the newly established MRC
Human Genome Resource Centre is now on the same site) and the National
Institute of Medical Research at Mill Hill, London bought a number of
SUN workstations and servers on the condition that SUN UK port the GCG
package to run on them until GCG start producing a UNIX version of their
own.
Version 5.3 was ported in 1989 and version 6.1 is currently being beta
tested.
Functionality:
The port is very close to the VAX/VMS version. Notable differences as
far as the general user is concerned are:
Instead of starting a command option with a '/', eg.
pepplot /col=1
it uses a minus sign '-' instead, in the normal UNIX convention, eg.
pepplot -col=1
VAX/VMS commands are case insensitive.
In the UNIX version all commands must be in lower case. The database
names and sequence names can be given in any case, eg.
fetch EMBL:Hscg1d
fetch embl:HSCG1D
When giving a wild-card set of sequence names on a command line, eg.
fetch EMBL:HSVBG*
one has to enclose the part of the command line with the asterisk in
double quotes to prevent the shell from attempting to match it to files
in the current directory, eg.
fetch "EMBL:HSVBG*"
Availability:
As far as general availability of this software, licences and prices
concerns please contact your nearest Sun Microsystems representative and
advise him to ask for details by e-mail from Paul Barrett, Sun district
sales manager in the Whetstone office in London, UK.
Portability:
SUN have made no effort to do anything other than get GCG running on
SUN4 machines for us. Specifically, the 'f77cvt' tool for aiding
conversions from VAX/VMS fortran to SUN4 fortran is used during
compilation, there are a few 'C' routines using conventions that are
possibly specific to SUN4 for calling C from fortran, SUN GKS is used
for the graphics routines.
Size:
About 170 Mbytes including the databases (both EMBL and GenBank are
currently held in full by our site) and with no attempt to compress the
sources and non-essential files. Maybe 120-150 Mbytes for a tidied-up
version.
If anybody is interested in seeing the software running in natura,
please let us know and we might organise a demonstration for you.
I have no affiliation or connection with SUN Microsystems.
Gary Williams
Computing Services Section, Janet: G.Williams at UK.AC.CRC
MRC-Clinical Research Centre, Elsewhere: G.Williams at CRC.AC.UK
Watford Rd, HARROW, Middx, HA1 3UJ, UK EARN/Bitnet: G.Williams%CRC at UKACRL
Tel 081-869 3294 Fax 081-423 1275 Usenet: ...!mcvax!ukc!mrccrc!G.Williams
