<commit_before># Ensembl module fohr Bio::EnsEMBL::Analysis::Config::Databases
#
# Copyright (c) 2006 Ensembl
#
# POD documentation - main docs before the code
#

=head1 NAME

Bio::EnsEMBL::Analysis::Config::Databases 

=head1 SYNOPSIS

    use Bio::EnsEMBL::Analysis::Config::Databases ; 

=head1 DESCRIPTION

Databases.pm 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
C<%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 C<%Config> to add or alter variables.

All the variables are in capitals, so that they resemble environment
variables. 

Databases is a pure ripoff of humConf written by <NAME>.
humConf is based upon ideas from the standard perl Env environment
module.


=head1 CONTACT

<EMAIL>

=cut

package Bio::EnsEMBL::Analysis::Config::Databases ; 

use strict;
use vars qw(%Config);

%Config= (


  DATABASES => { 
                  
                 # The REFERENCE_DB (formely known as GB_DB) holds sequence + repeats + features 
                 # from raw computes (e.g. ab-inito predictions, dna- or protein alignments ) 
                  
                 REFERENCE_DB => 
                                 { 
                                   -dbname => 'at6_system_test',
                                   -host => 'genebuild2',
                                   -port => '3306',
                                   -user => 'ensadmin',
                                   -pass => '<PASSWORD>',
                                  },
  
 
                 # The GENEWISE_DB holds genes made by FPC_TargettedGenewise or FPC_BlastMiniGenewise 
                 # (TGE_gw or similarity_genewise - genes ) ( formerly GB_GW_DB ) 

                 GENEWISE_DB => 
                                 { 
                                   -dbname => '',
                                   -host => '',<commit_msg>Left DB args blank for test system's users to fill in.<commit_after># Ensembl module fohr Bio::EnsEMBL::Analysis::Config::Databases
#
# Copyright (c) 2006 Ensembl
#
# POD documentation - main docs before the code
#

=head1 NAME

Bio::EnsEMBL::Analysis::Config::Databases 

=head1 SYNOPSIS

    use Bio::EnsEMBL::Analysis::Config::Databases ; 

=head1 DESCRIPTION

Databases.pm 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
C<%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 C<%Config> to add or alter variables.

All the variables are in capitals, so that they resemble environment
variables. 

Databases is a pure ripoff of humConf written by <NAME>.
humConf is based upon ideas from the standard perl Env environment
module.


=head1 CONTACT

<EMAIL>

=cut

package Bio::EnsEMBL::Analysis::Config::Databases ; 

use strict;
use vars qw(%Config);

%Config= (


  DATABASES => { 
                 # MUST AT LEAST FILL IN REFERENCE_DB DETAILS. THEY SHOULD BE THE SAME AS THOSE
                 # SPECIFIED IN ensembl-pipeline/test_system/TestDB.conf
                  
                 # The REFERENCE_DB (formely known as GB_DB) holds sequence + repeats + features 
                 # from raw computes (e.g. ab-inito predictions, dna- or protein alignments ) 
                  
                 REFERENCE_DB => 
                                 { 
                                   -dbname => '',
                                   -host => '',
                                   -port => '',
                                   -user => '',
                                   -pass => '',
                                  },
  
 
                 # The GENEWISE_DB holds genes made by FPC_TargettedGenewise or FPC_BlastMiniGenewise 
                 # (TGE_gw or similarity_genewise - genes ) ( formerly GB_GW_DB ) 

                 GENEWISE_DB => 
                                 { 
                                   -dbname => '',
                                   -host => '',
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