[ensembl-dev] Two simple questions about installation

Andy Yates ayates at ebi.ac.uk
Wed Mar 21 19:31:47 GMT 2012


Hi Jonathan,

If you want to bring Ensembl onto your lib programmatically you should path to the modules directory e.g.

use lib "/home/jonathan/Downloads/ensembl/modules";

To answer your second question you can bring the Ensembl Api onto your PERL5LIB environment variable before running the installation for InterlogWalk. As far as I remember InterlogWalk looks for the Registry object; so long as that's available at installation time everything should be fine. 

You may want to consult the readme file distributed with InterlogWalk for more detailed installation instructions.

Hope this has helped,

Andy

Sent from my mobile.

On 21 Mar 2012, at 11:25, jonathan myles <jonathanmyles1 at googlemail.com> wrote:

> I'm sorry to bother the list with these two questions, which I suspect
> are quite elementary loading questions
> 
> 1)
> 
> I downloaded the file
> 
> ensembl.tar.gz
> 
> to
> 
> /home/jonathan/Downloads
> 
> on my Ubunntu Desktop. I then gave the command
> 
> tar zvxf ensembl.tar.gz
> 
> in this directory, after which for example, the file
> /home/jonathan/Downloads/ensembl/modules/Bio/EnsEMBL/Registry.pm
> 
> contains the subroutine
> 
> load_registry_from_db
> 
> 
>  I then tried to run the program trial.pl
> 
> ===
> use lib "/home/jonathan/Downloads/ensembl/modules/Bio/EnsEMBL";
> use lib "/home/jonathan/Downloads/ensembl/modules/Bio/EnsEMBL/Registry";
> 
> 
> 
> my $registry = 'Bio::EnsEMBL::Registry';
> 
> 
> 
> 
> $registry->load_registry_from_db(
>  -host => 'ensembldb.ensembl.org',
>  -user => 'anonymous'
>                                 );
> 
> my $slice_adaptor = $registry->get_adaptor( "human", "core", "slice");
> my $chn = 1;
> 
> 
> my $slice = $slice_adaptor->fetch_by_region('chromosome',$chr,
>                                                          16924640,
>                                                          16924800);
> 
> my $genes = $slice->get_all_Genes();
> 
> while (my $gene = shift @{$genes} ){
> 
>    my $x= $gene->description();
> 
> 
> 
>    print $chn;
>    print "   ";
>    print $gene->start();
>    print "   ";
>    print $gene->end();
>    print "\n";
>    print $x;
>    print "\n";
> 
> }
> 
> ===
> 
> 
> but I get the error message
> Can't locate object method "load_registry_from_db" via package
> "Bio::EnsEMBL::Registry" (perhaps you forgot to load
> "Bio::EnsEMBL::Registry"?) at trial.pl line 11.
> 
> I'm obviously missing something really obvious, but I can't see it
> 
> 2) When I get this sorted out, I'd like to install the ensembl api s
> ifId installed from CPAN, as root, so that I can then install other
> software like
> Bio-Homology-InterologWalk directy from CPAN.  Can I do this by the command
> 
> 
> tar zvxf ensembl.tar.gz
> 
> as superuser in a given directory, and if so how do I find the
> location of this directory on my machine?
> 
> Again, aplogies for what I suspect are pretty stupid questions.
> 
> Jonathan
> 
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> List admin (including subscribe/unsubscribe): http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/




More information about the Dev mailing list