[Bioperl-l] error running load_seqdatabase.pl

Hilmar Lapp hlapp at gmx.net
Thu Dec 29 20:51:40 EST 2005

BTW since Sep 1 there is no default for the driver anymore in the 
script nor in Bio::DB::BioDB->new() (which you'd use to instantiate a 
$db handle in your own script). Deeper inside there is still an 
implementation module (Bio::DB::SimpleDBContext) that sets mysql as the 
default driver if neither driver nor dsn are provided.

I.e., what I'm saying is don't rely anymore on mysql being the default 
driver as this behavior may go away at any time - always specify it 

On another note, if you're always connecting to the same biosql 
instance, you may want to put a file .bioperldb in your home directory 
and use option --initrc. See the POD.


On Dec 29, 2005, at 5:26 PM, Torsten Seemann wrote:

>> I'm getting the following error while trying to run :
>> ./load_seqdatabase.pl -host localhost -dbname USBA -dbuser postgres 
>> -format
>> genbank NC_003076.gbk
>> MSG: failed to open connection: Can't connect to local MySQL server 
>> through
>> socket '/var/lib/mysql/mysql.sock' (2)
>> But I've a postgreSQL db and not a MySQL one...could anyone please 
>> guide me
>> troubleshoot this?
> Did you read the documentation for the load_seqdatabase.pl script?
> It's in the script itself!
>    =item --driver $driver
>    the DBI driver name for the RDBMS e.g., mysql, Pg, or Oracle [mysql]
> The default DBI driver is [mysql].
> I think you want the option "-driver Pg".
> -- 
> Torsten Seemann
> Victorian Bioinformatics Consortium, Monash University, Australia
> http://www.vicbioinformatics.com/
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757

More information about the Bioperl-l mailing list