Bio::EnsEMBL::Analysis::Config Databases
SummaryPackage variablesSynopsisDescriptionGeneral documentationMethods
WebCvsRaw content
Package variables
No package variables defined.
    use Bio::EnsEMBL::Analysis::Config::Databases ;
Description is the main configuration file which holds the different
parameters (usernames, hosts, passwords, ports, database-names) to
connect to different databases used in the Ensembl-Analysis pipeline.
It imports and sets a number of standard global variables into the
calling package. Without arguments all the standard variables are set,
and with a list, only those variables whose names are provided are set.
The module will die if a variable which doesn\'t appear in its
%Config hash is asked to be set.
A common way to get an DBAdaptor in a module is

print "Loading database : ". $$DATABASES{REFERENCE_DB}{"-dbname"} . "\n";
my $ref_db = new Bio::EnsEMBL::DBSQL::DBAdaptor( %{ $$DATABASES{REFERENCE_DB} }) ; OR if you write a RunnableDB: use Bio::EnsEMBL::Analysis::RunnableDB::BaseGeneBuild; @ISA = qw ( Bio::EnsEMBL::Analysis::RunnableDB::BaseGeneBuild ) my $genes_db = $self->get_dbadaptor("GENEBUILD_DB"); OR for normal scripts : use Bio::EnsEMBL::Analysis::Tools::Utilities qw( get_db_adaptor_by_string ); get_db_adaptor_by_string("GENEBUILD_DB") The variables can also be references to arrays or hashes.
Edit %Config to add or alter variables.
All the variables are in capitals, so that they resemble environment
Databases is a pure ripoff of humConf written by James Gilbert.
humConf is based upon ideas from the standard perl Env environment
No description
Methods description
None available.
Methods code
sub import {
    my ($callpack) = caller(0); # Name of the calling package
my $pack = shift; # Need to move package off @_
# Get list of variables supplied, or else all
my @vars = @_ ? @_ : keys(%Config); return unless @vars; # Predeclare global variables in calling package
eval "package $callpack; use vars qw(" . join(' ', map { '$'.$_ } @vars) . ")"; die $@ if $@; foreach (@vars) { if (defined $Config{ $_ }) { no strict 'refs'; # Exporter does a similar job to the following
# statement, but for function names, not
# scalar variables:
*{"${callpack}::$_"} =\$ Config{ $_ }; } else { die "Error: Config: $_ not known\n"; } } } 1;
General documentation