[Bioperl-l] error running load_seqdatabase.pl

[Hilmar Lapp]

No. Just in the base directory of your unpacked bioperl-db download 
type 'make test' (obviously without the quotes).

If you installed bioperl in a non-standard place make sure you set the 
PERL5LIB environment appropriately before doing this.

	-hilmar

On Dec 30, 2005, at 2:36 PM, Angshu Kar wrote:

> Also how to run the bioperl-db test ? I mean do I have to reinstall it 
> to run the make test command?
>
>
>
> On 12/30/05, Angshu Kar < angshu96 at gmail.com> wrote:Any clues why my 
> load_seqdatabase.pl (./load_seqdatabase.pl --dbname=USBA 
> --dbuser=postgres --format=genbank  --driver=Pg --debug  
> NC_003076.gbk)
>>  is getting killed after the follwoing step?
>>
>>  Using Bio::DB::BioSQL::Pg::BiosequenceAdaptorDriver as driver peer 
>> for Bio::DB::BioSQL::BiosequenceAdaptor
>> preparing SELECT statement: SELECT bioentry_id FROM biosequence WHERE 
>> bioentry_id = ?
>>
>> Killed
>>
>> I'm using a linux box. This didn't happen for a different i/p file!
>>
>> Thanks,
>> Angshu
>>
>>
>> On 12/29/05, Angshu Kar < angshu96 at gmail.com> wrote: I'm sorry that I 
>> missed it! Thanks for pointing it out.
>>> Also thanks Hilmar for the update.
>>>
>>> Angshu
>>>
>>>
>>> On 12/29/05, Torsten Seemann < 
>>> torsten.seemann at infotech.monash.edu.au > 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/
>>>
>>
>>
-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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