[ensembl-dev] Unable to connect to Compara->homology

Matthieu Muffato muffato at ebi.ac.uk
Thu Mar 20 09:38:31 GMT 2014


Dear Casper,

The message "Exception Can't locate feature.pm" means that Perl was not 
able to understand a "use feature qw(switch)" directive.

It looks like you are using Perl version 5.8.8. Since Ensembl 75, the 
APIs require Perl 5.10 (other parts of the project may require even more 
recent versions such as 5.14)

The get_adaptor() call should work if you upgrade your Perl installation.

Best regards,
Matthieu

On Wed 19 Mar 2014 23:46:57 GMT, Casper Shyr wrote:
> Hello,
>    I am having a problem creating the adaptor to the Ensembl compara’s
> homology database.
> *My code:*
> my $homology_adaptor = Bio::EnsEMBL::Registry->get_adaptor('Multi',
> 'compara', 'Homology');  die "homology  adaptor fail\n" if !defined
> $homology_adaptor;
> *
> *
> *My output:*
> *----------*---------- WARNING ----------------------
> MSG: 'Bio::EnsEMBL::Compara::DBSQL::HomologyAdaptor' cannot be found.
> Exception Can't locate feature.pm in @INC (@INC contains:
> /usr/local/src/ensembl-75/ensembl-funcgen/modules
> /usr/local/src/ensembl-75/ensembl-variation/modules
> /usr/local/src/ensembl-75/ensembl-compara/modules
> /usr/local/src/ensembl-75/ensembl/modules
> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi
> /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl
> /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi
> /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl
> /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8
> .) at
> /usr/local/src/ensembl-75/ensembl-compara/modules/Bio/EnsEMBL/Compara/AlignedMember.pm
> line 75.
> BEGIN failed--compilation aborted at
> /usr/local/src/ensembl-75/ensembl-compara/modules/Bio/EnsEMBL/Compara/AlignedMember.pm
> line 75.
> Compilation failed in require at
> /usr/local/src/ensembl-75/ensembl-compara/modules/Bio/EnsEMBL/Compara/AlignedMemberSet.pm
> line 86.
> BEGIN failed--compilation aborted at
> /usr/local/src/ensembl-75/ensembl-compara/modules/Bio/EnsEMBL/Compara/AlignedMemberSet.pm
> line 86.
> Compilation failed in require at (eval 234) line 3.
> ...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
> BEGIN failed--compilation aborted at
> /usr/local/src/ensembl-75/ensembl-compara/modules/Bio/EnsEMBL/Compara/Homology.pm
> line 76.
> Compilation failed in require at
> /usr/local/src/ensembl-75/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/HomologyAdaptor.pm
> line 24.
> BEGIN failed--compilation aborted at
> /usr/local/src/ensembl-75/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/HomologyAdaptor.pm
> line 24.
> Compilation failed in require at (eval 233) line 3.
>
>
> FILE: Bio/EnsEMBL/Registry.pm LINE: 1040
> CALLED BY: get_paralogs.pl  LINE: 45
> Date (localtime)    = Wed Mar 19 16:38:34 2014
> Ensembl API version = 75
> ---------------------------------------------------
>
> *Additional notes:*
> 1) I have already checked that the compara is installed and in my
> script, I already linked to the modules using:
> use lib '/usr/local/src/ensembl-75/ensembl-compara/modules’;
> use Bio::EnsEMBL::Registry;
>
> 2) The following code works:
> my $gene_member_adaptor = Bio::EnsEMBL::Registry->get_adaptor('Multi',
> 'compara', 'GeneMember'); die "gene member adaptor fail\n" if !defined
> $gene_member_adaptor;
> It seems that I can connect to GeneMember for compara no problem, but
> fails when I replace “GeneMember" with “Homology"
>
> Any suggestion is greatly appreciated! Thanks!
> Casper Shyr
> PhD Candidate, Centre for Molecular Medicine and Therapeutics
> University of British Columbia
> casper at cmmt.ubc.ca <mailto:casper at cmmt.ubc.ca>
>
>
>
>
>
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-- 
Matthieu Muffato, Ph.D.
Ensembl Developer and Ensembl Compara Manager
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus, Hinxton
Cambridge, CB10 1SD, United Kingdom
Room  A3-145
Phone + 44 (0) 1223 49 4631
Fax   + 44 (0) 1223 49 4468




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