[Bioclusters] Local copy of NCBI

Josh Goodman bioclusters@bioinformatics.org
Mon, 22 Sep 2003 12:39:59 -0500 (EST)

	In addition to the NCBI server you may want to take a look at our
database mirroring service at http://www.bio-mirror.net.  We offer most of
the NCBI dbs and other important dbs with mirrors all over the world.
Most servers support ftp and http but the USA server also mirrors data via
rsync.  If you don't see a database that you think we should have let us
know and we will try to get it up there.

Josh Goodman
Indiana University

Subject: Re: [Bioclusters] Local copy of NCBI
From: Nox <pheusion@snet.net>
To: bioclusters@bioinformatics.org
Cc: "Tang, Kevin" <kht7@cdc.gov>
Date: Thu, 18 Sep 2003 13:16:38 -0400
Reply-To: bioclusters@bioinformatics.org

We are using in-house perl scripts, in crontab, that
uses wget to pull updates from the DB.
Perl is great for parsing, so thats what my developers are using.

Unfortunatly I cant copy the script in here,
but I can tell you it relies on the wget heavily,
and  perl provides the transition  to populate our DB

Hope that helps

GenMicro Systems

On Thu, 2003-09-18 at 09:46, Osborne, John wrote:
> Hi everyone,
> What are people out there doing to get a local copy of NCBI's databases?  I
> mean RefSeq, dbSNP, taxonomy, etc...  We've been updating our copy ad-hoc by
> ftp, are most people just putting this into a cron job?
> I've heard that the NCBI tookkit offers something like this (to get daily
> updates via web services or something) but I don't know where to look.
> getseq looks suspicious but I need to configure it using entrez2, which
> needs X Windows, which needs vibrant, which means RH dependency hell...  Is
> there a simple commandline way to get get a seequence from NCBI and keep a
> local copy of NCBI?
>  -John
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> Bioclusters maillist  -  Bioclusters@bioinformatics.org
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