[BiO BB] Updating NCBI databases

[Ryan Golhar]

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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