[BiO BB] RE: BiO_Bulletin_Board Digest, Vol 10, Issue 9

Sat Aug 13 06:40:55 EDT 2005

Thanks Ryan,

I was going thru the email burst of BioBB and it got a good answer to an
email thru your email.

Rgds,

Indranil

-----Original Message-----
From: bio_bulletin_board-bounces+imitra=myezconnect.com at bioinformatics.org
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] On Behalf Of bio_bulletin_board-request at bioinformatics.org
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Subject: BiO_Bulletin_Board Digest, Vol 10, Issue 9

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Today's Topics:

   1. RE: BLAST: locally installed databases (Ryan Golhar)
   2. RE: BLAST: locally installed databases (Bossers, Alex)

----------------------------------------------------------------------

Message: 1
Date: Thu, 11 Aug 2005 12:09:45 -0400
From: Ryan Golhar <golharam at umdnj.edu>
Subject: RE: [BiO BB] BLAST: locally installed databases
To: 'Samantha Fox' <bioinfosm at gmail.com>,	"'The general forum at
	Bioinformatics.Org'"	<bio_bulletin_board at bioinformatics.org>
Message-ID: <002d01c59e8f$16f42c60$e6028a0a at GOLHARMOBILE1>
Content-Type: text/plain; charset="us-ascii"

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
>
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------------------------------

Message: 2
Date: Fri, 12 Aug 2005 07:23:43 +0200
From: "Bossers, Alex" <Alex.Bossers at wur.nl>
Subject: RE: [BiO BB] BLAST: locally installed databases
To: <golharam at umdnj.edu>, "The general forum at Bioinformatics.Org"
	<bio_bulletin_board at bioinformatics.org>
Message-ID:
	<839C6D97DA4B564882F385F1DA46742C037F8416 at slely0004.wurnet.nl>
Content-Type: text/plain;	charset="us-ascii"

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
> > _______________________________________________
> > 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
> >

------------------------------

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End of BiO_Bulletin_Board Digest, Vol 10, Issue 9
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