EnsemblGeneric_conf.pm

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=pod 
 
=head1 NAME
 
    Bio::EnsEMBL::Hive::PipeConfig::EnsemblGeneric_conf
 
=head1 DESCRIPTION
 
    Generic configuration module for all Ensembl-derived pipelines.
    It extends HiveGeneric_conf with specifically Ensembl things (knows about the release number, for instance).
 
    So if your pipeline has anything to do with Ensembl API/schema, please inherit (directly or not) your config from this file.
 
=head1 LICENSE
 
    Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
    Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
    Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License.
    You may obtain a copy of the License at
 
         http://www.apache.org/licenses/LICENSE-2.0
 
    Unless required by applicable law or agreed to in writing, software distributed under the License
    is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
    See the License for the specific language governing permissions and limitations under the License.
 
=head1 CONTACT
 
    Please subscribe to the Hive mailing list:  http://listserver.ebi.ac.uk/mailman/listinfo/ehive-users  to discuss Hive-related questions or to be notified of our updates
 
=cut
 
 
package Bio::EnsEMBL::Hive::PipeConfig::EnsemblGeneric_conf;
 
use strict;
use warnings;
 
use Bio::EnsEMBL::ApiVersion ();
 
use base ('Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf');
 
 
=head2 default_options
 
    Description : Interface method that should return a hash of option_name->default_option_value pairs.
                  Please see existing PipeConfig modules for examples.
 
=cut
 
sub default_options {
    my ($self) = @_;
    return {
        %{ $self->SUPER::default_options() },   # inherit from parent
 
            # Please note: ENVironment variables may be "exported" to inherit from enclosing shell,
            # but if you want to *prevent* that you need to specifically say so
            #  (setting a password to empty string does exactly that - sets it to an empty string)
            #
            #   [bash]      export -n ENSEMBL_CVS_ROOT_DIR  # will stop exporting, but the value in current shell stays as it was
            #   [tcsh]      unsetenv ENSEMBL_CVS_ROOT_DIR   # will destroy the variable even in current shell, and stop exporting
 
            # have to be careful not to check for $self->o('ensembl_cvs_root_dir') unless no env variable is set, or else
            # it will cause options missing errors. Also, the $self->o() system doesn't support optional options at
            # the time of this commit, so we can only have one of ensembl_root_dir or ensembl_cvs_root_dir, otherwise
            # there would always be an options missing error. We choose ensembl_cvs_root_dir for backwards compatibility.
        'ensembl_cvs_root_dir'  => defined($ENV{'ENSEMBL_ROOT_DIR'} || $ENV{'ENSEMBL_CVS_ROOT_DIR'}) ?
             $ENV{'ENSEMBL_ROOT_DIR'} || $ENV{'ENSEMBL_CVS_ROOT_DIR'} : $self->o('ensembl_cvs_root_dir'),
        'ensembl_root_dir'      => $self->o('ensembl_cvs_root_dir'),
        'ensembl_release'       => Bio::EnsEMBL::ApiVersion::software_version(),                        # snapshot of EnsEMBL Core API version. Please do not change if not sure.
        'rel_suffix'            => '',                                                                  # an empty string by default, a letter otherwise
        'rel_with_suffix'       => $self->o('ensembl_release').$self->o('rel_suffix'),
 
        'pipeline_name'         => $self->default_pipeline_name().'_'.$self->o('rel_with_suffix'),
 
        'user'                  => $ENV{'EHIVE_USER'} || 'ensadmin',
        'password'              => $ENV{'EHIVE_PASS'} // $ENV{'ENSADMIN_PSW'} // $self->o('password'),  # people will have to make an effort NOT to insert it into config files like .bashrc etc
    };
}
 
 
=head2 pipeline_wide_parameters
 
    Description : Interface method that should return a hash of pipeline_wide_parameter_name->pipeline_wide_parameter_value pairs.
                  The value doesn't have to be a scalar, can be any Perl structure now (will be stringified and de-stringified automagically).
                  Please see existing PipeConfig modules for examples.
 
=cut
 
sub pipeline_wide_parameters {
    my ($self) = @_;
    return {
        %{ $self->SUPER::pipeline_wide_parameters() },      # inherit from parent
 
#        'schema_version' => $self->o('ensembl_release'),   # commented out to avoid duplicating 'schema_version' inserted by the schema mysql file
    };
}
 
1;