[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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