[ensembl-dev] Two simple questions about installation

jonathan myles jonathanmyles1 at googlemail.com
Wed Mar 21 11:25:11 GMT 2012


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




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