[Info-gcg] GCG 11.0

Michael Black mbb8n at virginia.edu
Wed Sep 7 18:20:25 EST 2005

Is anyone else frustrated with GCG 11.0 and Seqweb 3.0?

My first peeve (which I've communicated to Accelrys) was the lack of 
printed documentation - not the program docs, but the admin docs.  Those 
should have been provided in printed format.

Second, I learned today, that dbnamemap.conf is now case sensitive, 
which is not documented, and its predecessor never was.  An example, we 
have the C. elegans database locally - I named the sections "worm_I", 
"worm_II", and so forth.  But 11.0 only works with them if the 
chromosome roman numbers are lower case - which was never the case with 
GCG 10.0 through 10.3.

Another example - admins of GCG 10 are familiar with the gcgdata 
directory (which in our case held sym links to our database 
directories).  In 11.0, there is a "db" directory, which is blank - no 
documentation on what it's there for, why it exists, nothing (should it 
hold sym links to the database files - ours are on a RAID?).  What the 
heck is it for, since .conf files seem to cover all that now?

GCGSRS appears to need a ".wp" directory and files (for gcgadmin) to 
work correctly (that was the case for the patch for 10.3, which I only 
learned about 4 months after it was released), but this directory is not 
created by default with the install of II.0?

We are still running GCG 10.3 for our users, and have CAREFULLY followed 
the install instructions for 11.0, and running it at the same time.  
Yet, when I invoke GCGSUPPORt for 11.0, I still have to move into "sbin" 
and run utils directly from there - sbin does not seem to be added to 
paths when GCG 11.0 is sourced in at startup?

We have not even gotten into SeqWeb 3.0, but will shortly.

So far the transition has not gone smoothly.  I've had to futz with a 
lot of .conf files, discovering things about their syntax that is not 

Has anyone had a smooth transition from 10.3 to 11.0?  We run GCG on a 
SunFire 480 (dual cpu's, 10GB RAM - databases are on an Apple XRAID - 
about 1.98TB total, sliced into two ~917+GB wedges).  We do not 
subscribe to any Accelry's database service - do that ourselves (PERL 
scripts), and do have a lot of custom db's (ie. not just the regular 
NCBI ones, nor just UniProt).  So our db conf files are non-standard.  
But, still, simple things like case sensitivity aren't even documented, 
after years of not being so.  This irritates me.

Just looking for observations/comments about 11.0 from admins.

Cheers, Michael
Michael B. Black, Ph.D.
Molecular Biology Computing Support
University of Virginia
ITC-Academic Computing Health Sciences

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