[BiO BB] Updating NCBI databases

Samantha Fox bioinfosm at gmail.com
Sat Mar 4 17:58:23 EST 2006

Thanks for the note !
Yeah, I cant think of other options for now .. but will let you know if I
figure something.


On 2/8/06, Ryan Golhar <golharam at umdnj.edu> wrote:
> I think the easiest way is to do a 'ps -ef | grep blast'.  If it returns a
> process (other than itself) in the list, then you know someone is running
> blast.
> The other (simpler) option is to maintain a seperate BLAST database that
> you can copy in place under a standard maintainence window.  We normally
> reboot our server once a month when system patches are applied.  During this
> outage period, the new database could be copied in place.
> Let me know what you end up doing.  I'm curious to the solution you decide
> on.  I might want to use that here.
> Ryan
> -----Original Message-----
> *From:* bio_bulletin_board-bounces+golharam=umdnj.edu at bioinformatics.org[mailto:
> bio_bulletin_board-bounces+golharam=umdnj.edu at bioinformatics.org] *On
> Behalf Of *Samantha Fox
> *Sent:* Tuesday, February 07, 2006 12:16 PM
> *To:* The general forum at Bioinformatics.Org
> *Subject:* [BiO BB] Updating NCBI databases
> Hi,
> I had a question regarding regular update of BLAST databases. Is there a
> standard way to move the updated databases to the user section, making sure
> that the current copy is not already in use ?
> Suppose I update the database monthly, but a user might have a big BLAST
> job running when my cron script starts the update. This can lead to errors.
> How can I prevent that ?
> Thanks,
> ~S
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