Hello, it seems like your path points to rc6. The rc6 is a java version of the BioMart code and you are trying to run the Perl one? Please make sure to include biomart-perl libs in your path
a On 28 May 2013 11:28, arubio <[email protected]> wrote: > > > Hello, I installed the biomart following the steps described in > http://www.biomart.org/**download.html<http://www.biomart.org/download.html> > > I need to run the code i show at the end of this mail, in a .pl flie, > from the command line (prompt) and i get the error: > > ########### > Can't locate BioMart/Initializer.pm in @INC (@INC contains: > /home/arubio/Ensembl/bioperl-**1.2.3 /home/arubio/Ensembl/ensembl/**modules > /home/arubio /Ensembl/ensembl-compara/**modules > /home/arubio/Ensembl/ensembl-**variation/modules > /home/arubio/Ensembl/ensembl-**functgenomics/modules > /home/arubio/Biomart/biomart-**rc6 /usr/local/lib64/perl5 > /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl > /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at > bio.pl line 5. > BEGIN failed--compilation aborted at bio.pl line 5. > ########### > > I have include "PERL5LIB=${PERL5LIB}:${HOME}/**Biomart/biomart-rc6" in > bashrc file. > > What can i do? > > thanks > > > > bio.pl->>>> > > # An example script demonstrating the use of BioMart API. > # This perl API representation is only available for configuration > versions >= 0.5 > use strict; > use BioMart::Initializer; > use BioMart::Query; > use BioMart::QueryRunner; > > my $confFile = "PATH TO YOUR REGISTRY FILE UNDER biomart-perl/conf/. For > Biomart Central Registry navigate to > http://www.biomart.org/** > biomart/martservice?type=**registry<http://www.biomart.org/biomart/martservice?type=registry> > "; > # > # NB: change action to 'clean' if you wish to start a fresh configuration > # and to 'cached' if you want to skip configuration step on subsequent > runs from the same registry > # > > my $action='cached'; > my $initializer = BioMart::Initializer->new('**registryFile'=>$confFile, > 'action'=>$action); > my $registry = $initializer->getRegistry; > > my $query = BioMart::Query->new('registry'**=>$registry,'** > virtualSchemaName'=>'default')**; > > > $query->setDataset("hsapiens_**gene_ensembl"); > $query->addAttribute("ensembl_**gene_id"); > $query->addAttribute("ensembl_**transcript_id"); > $query->addAttribute("atlas_**celltype"); > $query->addAttribute("atlas_**diseasestate"); > $query->addAttribute("atlas_**organismpart"); > > $query->formatter("TSV"); > > my $query_runner = BioMart::QueryRunner->new(); > ############################## GET COUNT ############################ > # $query->count(1); > # $query_runner->execute($query)**; > # print $query_runner->getCount(); > ##############################**##############################**######### > > > ############################## GET RESULTS ########################## > # to obtain unique rows only > # $query_runner->uniqueRowsOnly(**1); > > $query_runner->execute($query)**; > $query_runner->printHeader(); > $query_runner->printResults(); > $query_runner->printFooter(); > ##############################**##############################**######### > > ______________________________**_________________ > Users mailing list > [email protected] > https://lists.biomart.org/**mailman/listinfo/users<https://lists.biomart.org/mailman/listinfo/users> >
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