[Bioclusters] Local copy of NCBI

Nox bioclusters@bioinformatics.org
Thu, 18 Sep 2003 13:16:38 -0400

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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