[BiO BB] BLAST: locally installed databases

[Ryan Golhar]

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
> _______________________________________________
> Bioinformatics.Org general forum  - 
> BiO_Bulletin_Board at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
> 
> _______________________________________________
> Bioinformatics.Org general forum  -  
> BiO_Bulletin_Board at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: get_nr.pl
Type: application/octet-stream
Size: 1680 bytes
Desc: not available
URL: <http://www.bioinformatics.org/pipermail/bbb/attachments/20050811/33b48702/attachment.obj>