<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:"Bitstream Vera Sans [bitstream]", "helvetica", sans-serif;font-size:13pt"><DIV>Hi Gautier,<BR></DIV><DIV><BR></DIV><DIV>Here is my PERL5LIB config:</DIV><DIV><BR></DIV><DIV>[root@bxiew ~]# echo $PERL5LIB<BR>:/src/bioperl-live:/src/ensembl/modules:/src/ensembl-compara/modules:/src/ensembl-variation/modules:/src/ensembl-functgenomics/modules:/usr/primer3-1.1.4/src<BR></DIV><DIV><BR></DIV><DIV>Are they right?</DIV><DIV><BR></DIV><DIV>Thanks,</DIV><DIV>Grace</DIV><DIV style="font-family:arial, helvetica, sans-serif;font-size:13pt"><BR><DIV style="font-family:arial, helvetica, sans-serif;font-size:13px"><FONT size="2" face="Tahoma"><HR size="1"><B><SPAN style="font-weight: bold;">寄件人﹕</SPAN></B> Gautier Koscielny <koscieln@ebi.ac.uk><BR><B><SPAN style="font-weight: bold;">收件人﹕</SPAN></B> Grace Cheng
<himwo@yahoo.com.hk><BR><B><SPAN style="font-weight: bold;">副本(CC)</SPAN></B> Abel Ureta-Vidal <abel@eaglegenomics.com>; dev ensembl <dev@ensembl.org><BR><B><SPAN style="font-weight: bold;">傳送日期﹕</SPAN></B> 2010/8/5 (四) 5:59:40 PM<BR><B><SPAN style="font-weight: bold;">主題：</SPAN></B> Re: [ensembl-dev] Re： Re： Re： Can't connect to ensembl database<BR></FONT><BR>Hello Grace,<BR><BR>Please, could you send your PERL5LIB configuration (echo $PERL5LIB).<BR><BR>rgds,<BR><BR>-Gautier-<BR><BR><BR>On 05/08/2010 10:55, Grace Cheng wrote:<BR>> Hi Abel,<BR>> <BR>> Here is what I get:<BR>> <BR>> [GraceCheng@bxiew Desktop]$ DBD::mysql::db selectall_arrayref failed: fetch() without execute() at /src/ensembl/modules/Bio/EnsEMBL/Registry.pm line 1418.<BR>> Will only load v58 databases<BR>> Bio::EnsEMBL::Variation::DBSQL::DBAdaptor module not found so variation databases will be ignored if found<BR>>
Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor module not found so functional genomics databases will be ignored if found<BR>> No Compara databases found<BR>> No ancestral database found<BR>> No GO database found<BR>> <BR>> Thanks,<BR>> Grace<BR>> <BR>> ------------------------------------------------------------------------<BR>> *寄件人﹕* Abel Ureta-Vidal <<A ymailto="mailto:abel@eaglegenomics.com" href="mailto:abel@eaglegenomics.com">abel@eaglegenomics.com</A>><BR>> *收件人﹕* Grace Cheng <<A ymailto="mailto:himwo@yahoo.com.hk" href="mailto:himwo@yahoo.com.hk">himwo@yahoo.com.hk</A>><BR>> *副本(CC)* dev ensembl <<A ymailto="mailto:dev@ensembl.org" href="mailto:dev@ensembl.org">dev@ensembl.org</A>><BR>> *傳送日期﹕* 2010/8/5 (四) 3:11:46 AM<BR>> *主題：* Re: [ensembl-dev] Re： Re： Can't connect to ensembl database<BR>> <BR>> What do you get with -verbose?<BR>> <BR>>
Abel<BR>> <BR>> On 4 Aug 2010, at 19:49, Grace Cheng wrote:<BR>> <BR>>> Hi Abel,<BR>>> <BR>>> <BR>>> Thanks for your help. I get the things below:<BR>>> <BR>>> <BR>>> [GraceCheng@bxiew Desktop]$ grep API_VERSION /src/ensembl/modules/Bio/EnsEMBL/Registry.pm<BR>>> my $API_VERSION = 58;<BR>>> return $API_VERSION;<BR>>> if ( $database_version != $API_VERSION ) {<BR>>> $API_VERSION, $database_version<BR>>> <BR>>> That mean I am in the right version, v58? I am really stuck in this point........<BR>>> <BR>>> <BR>>> Grace<BR>>> <BR>>> <BR>>> _______________________________________________<BR>>> Dev mailing list<BR>>> <A ymailto="mailto:Dev@ensembl.org" href="mailto:Dev@ensembl.org">Dev@ensembl.org</A> <mailto:<A ymailto="mailto:Dev@ensembl.org"
href="mailto:Dev@ensembl.org">Dev@ensembl.org</A>><BR>>> <A href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</A><BR>> <BR>> *__*<BR>> *Abel Ureta-Vidal*<BR>> *Eagle Genomics Ltd* | E: <A ymailto="mailto:abel@eaglegenomics.com" href="mailto:abel@eaglegenomics.com">abel@eaglegenomics.com</A> <mailto:<A ymailto="mailto:abel@eaglegenomics.com" href="mailto:abel@eaglegenomics.com">abel@eaglegenomics.com</A>><BR>> <A href="http://www.eaglegenomics.com" target="_blank">http://www.eaglegenomics.com</A> <<A href="http://www.eaglegenomics.com/" target="_blank">http://www.eaglegenomics.com/</A>><BR>> <BR>> <BR>> <BR>> _______________________________________________<BR>> Dev mailing list<BR>> <A ymailto="mailto:Dev@ensembl.org" href="mailto:Dev@ensembl.org">Dev@ensembl.org</A><BR>> <A href="http://lists.ensembl.org/mailman/listinfo/dev"
target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</A><BR>> <BR><BR><BR>-- Best Regards/Cordialement/Mit freundlichen Grüßen<BR>Gautier Koscielny, Ph.D.<BR>phone: +44 (0)1223 494 650<BR>EMBL Outstation - The European Bioinformatics Institute<BR>Wellcome Trust Genome Campus<BR>Hinxton CB10 1SD<BR>UK<BR><BR></DIV></DIV>
</div><br>
</body></html>