In article <5k4vl7$dqk$1 at dns.ktb.net>,
Albert Gold <bgold at ktb.net> writes:
> I am looking into a SUN Sparc. or Ultra as the least expensive
> alternatives to serve a group of 8 or so users.
> Pity GCG doesn't support Linux or FreeBSD...
> GCG recommends 64 meg of RAM. Why buy more?
> It is advisable if you want to run X to its full advantage: Unless
you stay at vanilla X, when you add Motif, CDE, multiple sessions/
programs, multiple users, etc... it gets hungry. If you add to it
a few memory eater programs like fold, pileup, etc... then it is
better not to be on the swap (virtual memory) side but on the RAM
one.
> GCG also tells me that 8 gigs of hard disk is sufficient to reformat
> publicly accessible GenBank data, but 4 gigs is sufficient to
> run with their formats (if purchased).
> You'll never have enough space. Databases are growing so fast.
OTOH, you shouldn't need much additional space to update your databases.
Actually, unless you want to keep an old copy while creating the new
version, you don't need any additional space at all beyond what the
formatted GCG libraries require.
> Can someone supply details on reformatting and can someone
> explain where to access the publicly available GenBank and other
> data for GCG reformatting purposes.
> Reformatting is easy. The traditional way -and less tricky- is
to get a local copy of the databases inraw format, and then run
the reformatting process to get the new copy. If you don't want
to disrupt users, then the new copy must coexsist with the old. This
implies 3x the size of the database. The basic procedure would be
1) xxxxtoGCG (e.g. embltogcg) to convert the old database to
the new format
2) seqcat to create the catalog files for stringsearch et al.
3) accessionnumbers to index the accession numbers
With a few simple UNIX tricks you can cut down that quite a lot.
Down to -if you don't mind updating the databases in place- no
additional space at all. I'm now refining my scripts so as to be able
to make then more general purpose for publication. *Iff* I get to
do that, then I'll try to share them.
jr
--
Jose R. Valverde
EMBnet/CNB
