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GCG Genbank database size

Mike Cherry cherry at fafner.Stanford.EDU
Fri May 10 10:11:24 EST 1996


In article <31930D15.794B at icrf.icnet.uk>,
Alex Whittaker - BIU  <A.Whittaker at icrf.icnet.uk> wrote:
>...
>GCG distributed database has exceeded 2Gb - the GenBank release 94.0 is
>listed as 4206466 Blocks - and this is quite a watershed.  In the first
>...
>
>  My sysadmin has pointed out another problem however, the limit of disk
>size mountable under most 32 bit operating systems is 2Gb.  Now this is
>...
>
>  Unless anyone can offer a simple solution, I think that GCG need to
>look into this with some urgency.  I would appreciate it if any
>responses could be cc: to me via e-mail as well as to this group.

We keep partitions less that 2Gb as that is a limit in nfs.  Its
really no big deal to edit the GCG configuration to use any number of
disk partitions for data sets.  I currently have GenBank spread over
four 2Gb disks.  Check out your gcgcore/script/gcguserspecs, I have:

Gb_New                     GenBankDir:gb_new
Gb_Ba                      GenBankDir:gb_ba
Gb_Est1                    GenBank2Dir:gb_est1
Gb_Est2                    GenBank2Dir:gb_est2
Gb_Est3                    GenBank2Dir:gb_est3
Gb_Est4                    GenBank3Dir:gb_est4
Gb_Est5                    GenBank3Dir:gb_est5
Gb_Est6                    GenBank4Dir:gb_est6
Gb_In                      GenBankDir:gb_in
Gb_Om                      GenBank4Dir:gb_om
Gb_Ov                      GenBank4Dir:gb_ov
...

You probably have everything going to GenBankDir.  Just find the
location for the definition of GenBankDir, which will reference
GenGenBankRoot and make a few new names.

After you reformat a GenBank section with the GCG commands it will go
into GenBankDir, you will need to move it the partition of choice, but
once in place GCG does not care that the data sets are scattered over
several disks.  The size of the total GenBank is not a problem for
GCG.

Mike

J. Michael Cherry                       Internet: cherry at genome.stanford.edu
Department of Genetics                  Stanford University School of Medicine
Medical Center, Room M311               Stanford, California  94305-5120
Voice: 415-723-7541                     FAX: 415-723-7016
-- 
J. Michael Cherry                       Internet: cherry at genome.stanford.edu
Department of Genetics                  Stanford University School of Medicine
Medical Center, Room M311               Stanford, California  94305-5120
Voice: 415-723-7541                     FAX: 415-723-7016



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