In article <5k76s2$k6u at acebo.sdi.uam.es>,(José R. Valverde) wrote:
> 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
> ....
> 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.
For starters, you might like to see:
http://www.embnet.org/embnet.news/vol2_3/tips.html
a noddy script which indexes each division in turn and so minimises
transitory disk requirement. An annoying oddity in GCG 8 was that
genbanktogcg allowed an -out= parameter, but that embltogcg didn't.
Now tell me: has that been fixed in GCG 9 ?
EMBL (inherently smaller than Genbank by perhaps 10-20%) 50 takes
3.2GB in GCG format. Doubling time is now ??? 8 months ? For a
five year DB storage plan you should arrange to mortgage your
institution or buy Lotto tickets and a really effective prayerwheel.
Andrew
--
Andrew T. Lloyd Irish National Centre for BioInformatics INCBI
atlloyd at acer.gen.tcd.iehttp://acer.gen.tcd.ie
Tel: (+353)-1-608-1969 EMBnet Ireland Fax: (+353)-679-8558
