Inheritance diagram for Bio::EnsEMBL::Hive::PipeConfig::EnsemblGeneric_conf:

Public Member Functions
public	default_options ()

public	pipeline_wide_parameters ()

Public Member Functions inherited from Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf
public	default_options ()

public	pipeline_create_commands ()

public	pipeline_wide_parameters ()

public	resource_classes ()

public	pipeline_analyses ()

public	beekeeper_extra_cmdline_options ()

public	hive_meta_table ()

public	pre_options ()

public	dbconn_2_url ()

public	pipeline_url ()

public	db_cmd ()

public	print_debug ()

public	process_pipeline_name ()

public	default_pipeline_name ()

public	process_options ()

public	overridable_pipeline_create_commands ()

public	is_analysis_topup ()

public	run_pipeline_create_commands ()

public	add_objects_from_config ()

public	useful_commands_legend ()

Public Member Functions inherited from Bio::EnsEMBL::Hive::DependentOptions
public	new ()

public	use_cases ()

public	load_cmdline_options ()

public	root ()

public	is_fully_substituted_string ()

public	is_fully_substituted_structure ()

public	hash_leaves ()

public	o ()

public	substitute ()

public	merge_from_rules ()

public	process_options ()

Detailed Description

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.

Definition at line 14 of file EnsemblGeneric_conf.pm.

Member Function Documentation

◆ default_options()

public Bio::EnsEMBL::Hive::PipeConfig::EnsemblGeneric_conf::default_options ( )

    Description : Interface method that should return a hash of option_name->default_option_value pairs.
                  Please see existing PipeConfig modules for examples.

Code:

click to view

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
    };
}

◆ pipeline_wide_parameters()

public Bio::EnsEMBL::Hive::PipeConfig::EnsemblGeneric_conf::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.