[BiO BB] BLAST: locally installed databases

Ryan Golhar golharam at umdnj.edu
Mon Aug 15 13:54:21 EDT 2005


NCBI says to download the databases in whole.  They don't do the
incremental updates anymore...not sure why...



-----Original Message-----
From: Bossers, Alex [mailto:Alex.Bossers at wur.nl] 
Sent: Friday, August 12, 2005 1:24 AM
To: golharam at umdnj.edu; The general forum at Bioinformatics.Org
Subject: RE: [BiO BB] BLAST: locally installed databases


What happened to the incremental updates to blastDb anyway? Alex


> -----Oorspronkelijk bericht-----
> Van: bio_bulletin_board-bounces+alex.bossers=wur.nl at bioinformatics.org
>
[mailto:bio_bulletin_board-bounces+alex.bossers=wur.nl at bioinformatics.or
g]
> Namens Ryan Golhar
> Verzonden: donderdag 11 augustus 2005 18:10
> Aan: 'Samantha Fox'; 'The general forum at Bioinformatics.Org'
> Onderwerp: RE: [BiO BB] BLAST: locally installed databases
> 
> Attached is the file get_nr.pl which will download the nr and nt 
> database from NCBI to the local machine as root to the directory 
> /usr/local/ncbi/db.
> 
> It does this by comparing the .tar.gz file timestamp on NCBI with the 
> one on your local machine.  If the one on NCBI is newer, the file is 
> downloaded.
> 
> The script is pretty simply and should get you going.  If you have any

> questions, let me know and I'll answer what I can.  It was written for

> Solaris, so you might need to change paths to some stuff for other 
> environments as well as download location...
> 
> Good luck,
> 
> Ryan
> 
> -----Original Message-----
> From: Samantha Fox [mailto:bioinfosm at gmail.com]
> Sent: Thursday, August 11, 2005 11:51 AM
> To: golharam at umdnj.edu; The general forum at Bioinformatics.Org
> Subject: Re: [BiO BB] BLAST: locally installed databases
> 
> 
> That will help Ryan. Thanks.
> And these are pre-formatted databases? And my guess is they goto the 
> data folder specified in .ncbirc ?
> 
> Thanks again,
> Sumit
> 
> On 8/11/05, Ryan Golhar <golharam at umdnj.edu> wrote:
> > I have a perl script running as a cron job to download the databases

> > nightly if there are new tarballs available....
> >
> > I can email you the script...
> >
> >
> > -----Original Message-----
> > From:
bio_bulletin_board-bounces+golharam=umdnj.edu at bioinformatics.org
> >
[mailto:bio_bulletin_board-bounces+golharam=umdnj.edu at bioinformatics.o
> > rg
> > ] On Behalf Of Samantha Fox
> > Sent: Thursday, August 11, 2005 11:09 AM
> > To: bio_bulletin_board at bioinformatics.org
> > Subject: [BiO BB] BLAST: locally installed databases
> >
> >
> > Hello,
> > I wish to have regularly updated databases from NCBI to use with my 
> > blastall command.
> >
> > Is there an easy standard way to do so ?
> >
> > Thanks,
> >
> > Samantha
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