[ensembl-dev] Re： Re： Re： Re： Can't connect to ensembl database

[Grace Cheng]

Hi Gautier,


Here is my PERL5LIB config:

[root at bxiew ~]# echo $PERL5LIB
:/src/bioperl-live:/src/ensembl/modules:/src/ensembl-compara/modules:/src/ensembl-variation/modules:/src/ensembl-functgenomics/modules:/usr/primer3-1.1.4/src



Are they right?

Thanks,
Grace



________________________________
寄件人﹕ Gautier Koscielny <koscieln at ebi.ac.uk>
收件人﹕ Grace Cheng <himwo at yahoo.com.hk>
副本(CC) Abel Ureta-Vidal <abel at eaglegenomics.com>; dev ensembl <dev at ensembl.org>
傳送日期﹕ 2010/8/5 (四) 5:59:40 PM
主題： Re: [ensembl-dev] Re：   Re： Re： Can't connect to ensembl database

Hello Grace,

Please, could you send your PERL5LIB configuration (echo $PERL5LIB).

rgds,

-Gautier-


On 05/08/2010 10:55, Grace Cheng wrote:
> Hi Abel,
> 
> Here is what I get:
> 
> [GraceCheng at bxiew Desktop]$ DBD::mysql::db selectall_arrayref failed: fetch() 
>without execute() at /src/ensembl/modules/Bio/EnsEMBL/Registry.pm line 1418.
> Will only load v58 databases
> Bio::EnsEMBL::Variation::DBSQL::DBAdaptor module not found so variation 
>databases will be ignored if found
> Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor module not found so functional genomics 
>databases will be ignored if found
> No Compara databases found
> No ancestral database found
> No GO database found
> 
> Thanks,
> Grace
> 
> ------------------------------------------------------------------------
> *寄件人﹕* Abel Ureta-Vidal <abel at eaglegenomics.com>
> *收件人﹕* Grace Cheng <himwo at yahoo.com.hk>
> *副本(CC)* dev ensembl <dev at ensembl.org>
> *傳送日期﹕* 2010/8/5 (四) 3:11:46 AM
> *主題：* Re: [ensembl-dev] Re： Re： Can't connect to ensembl database
> 
> What do you get with -verbose?
> 
> Abel
> 
> On 4 Aug 2010, at 19:49, Grace Cheng wrote:
> 
>> Hi Abel,
>> 
>> 
>> Thanks for your help. I get the things below:
>> 
>> 
>> [GraceCheng at bxiew Desktop]$ grep API_VERSION 
>>/src/ensembl/modules/Bio/EnsEMBL/Registry.pm
>> my $API_VERSION = 58;
>>   return $API_VERSION;
>>   if ( $database_version != $API_VERSION ) {
>>         $API_VERSION, $database_version
>> 
>> That mean I am in the right version, v58? I am really stuck in this 
>>point........
>> 
>> 
>> Grace
>> 
>> 
>>  _______________________________________________
>> Dev mailing list
>> Dev at ensembl.org <mailto:Dev at ensembl.org>
>> http://lists.ensembl.org/mailman/listinfo/dev
> 
> *__*
> *Abel Ureta-Vidal*
> *Eagle Genomics Ltd* | E: abel at eaglegenomics.com 
><mailto:abel at eaglegenomics.com>
> http://www.eaglegenomics.com <http://www.eaglegenomics.com/>
> 
> 
> 
> _______________________________________________
> Dev mailing list
> Dev at ensembl.org
> http://lists.ensembl.org/mailman/listinfo/dev
>    


-- Best Regards/Cordialement/Mit freundlichen Grüßen
Gautier Koscielny, Ph.D.
phone: +44 (0)1223 494 650
EMBL Outstation - The European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton CB10 1SD
UK


      
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20100809/b9a76c6c/attachment.html>