<commit_before>=head1 LICENSE

Copyright [1999-2016] EMBL-European Bioinformatics Institute
and Wellcome Trust Sanger 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.

=cut


=pod

=head1 NAME

Bio::EnsEMBL::Production::Pipeline::PipeConfig::XrefProjection_conf

=head1 DESCRIPTION

Configuration for running the Post Compara pipeline, which
run the Gene name, description and GO projections as well as Gene coverage.

=head1 Author

<NAME>

=cut

package Bio::EnsEMBL::Production::Pipeline::PipeConfig::XrefProjection_conf;

use strict;
use warnings;
use base ('Bio::EnsEMBL::Production::Pipeline::PipeConfig::PostCompara_conf');
use Bio::EnsEMBL::ApiVersion qw/software_version/;

sub default_options {
    my ($self) = @_;

    return {
        # inherit other stuff from the base class
        %{ $self->SUPER::default_options() },
        
	# division for GO & GeneName projection
	division_name     => '', # Eg: protists, fungi, plants, metazoa
        pipeline_name     => $self->o('ENV','USER').'_XrefProjections_'.$self->o('ensembl_release'),
        output_dir      => '/lustre/scratch109/ensembl/'.$self->o('ENV', 'USER').'/workspace/'.$self->o('pipeline_name'),
	email => $self->o('ENV', '<EMAIL>').'<EMAIL>',
	## Flags controlling sub-pipeline to run
	    # '0' by default, set to '1' if this sub-pipeline is needed to be run
    	flag_GeneNames    => '1',
    	flag_GeneDescr    => '1',
    	flag_GO           => '1',     
    	flag_GeneCoverage => '0',

    ## Flags controlling dependency between GeneNames & GeneDescr projections
        # '0' by default, 
        #  set to '1' to ensure GeneDescr starts after GeneNames completed
        flag_Dependency   => '1',     

    ## Flag controlling the way the projections will run
        # If the parallel flag is on, all the projections will run at the same time
        # If the parallel flag is off, the projections will run sequentially, one set of projections at the time.
        # Default value is 1
        parallel_GeneNames_projections => '0',
        parallel_GO_projections       => '0',
    ## analysis_capacity values for some analyses:
        geneNameproj_capacity  =>  '20',
        geneDescproj_capacity  =>  '20',
        goProj_capacity        =>  '20',
        geneCoverage_capacity  =>  '100',

    ## Flag controling the use of the is_tree_compliant flag from the homology table of the Compara database
    ## If this flag is on (=1) then the pipeline will exclude all homologies where is_tree_compliant=0 in the homology table of the Compara db<commit_msg>Not projecting GO by default since we are now getting these via the GOA import pipeline<commit_after>=head1 LICENSE

Copyright [1999-2016] EMBL-European Bioinformatics Institute
and Wellcome Trust Sanger 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.

=cut


=pod

=head1 NAME

Bio::EnsEMBL::Production::Pipeline::PipeConfig::XrefProjection_conf

=head1 DESCRIPTION

Configuration for running the Post Compara pipeline, which
run the Gene name, description and GO projections as well as Gene coverage.

=head1 Author

<NAME>

=cut

package Bio::EnsEMBL::Production::Pipeline::PipeConfig::XrefProjection_conf;

use strict;
use warnings;
use base ('Bio::EnsEMBL::Production::Pipeline::PipeConfig::PostCompara_conf');
use Bio::EnsEMBL::ApiVersion qw/software_version/;

sub default_options {
    my ($self) = @_;

    return {
        # inherit other stuff from the base class
        %{ $self->SUPER::default_options() },
        
	# division for GO & GeneName projection
	division_name     => '', # Eg: protists, fungi, plants, metazoa
        pipeline_name     => $self->o('ENV','USER').'_XrefProjections_'.$self->o('ensembl_release'),
        output_dir      => '/lustre/scratch109/ensembl/'.$self->o('ENV', 'USER').'/workspace/'.$self->o('pipeline_name'),
	email => $self->o('ENV', 'USER').'<EMAIL>',
	## Flags controlling sub-pipeline to run
	    # '0' by default, set to '1' if this sub-pipeline is needed to be run
    	flag_GeneNames    => '1',
    	flag_GeneDescr    => '1',
    	flag_GO           => '0',     
    	flag_GeneCoverage => '0',

    ## Flags controlling dependency between GeneNames & GeneDescr projections
        # '0' by default, 
        #  set to '1' to ensure GeneDescr starts after GeneNames completed
        flag_Dependency   => '1',     

    ## Flag controlling the way the projections will run
        # If the parallel flag is on, all the projections will run at the same time
        # If the parallel flag is off, the projections will run sequentially, one set of projections at the time.
        # Default value is 1
        parallel_GeneNames_projections => '0',
        parallel_GO_projections       => '0',
    ## analysis_capacity values for some analyses:
        geneNameproj_capacity  =>  '20',
        geneDescproj_capacity  =>  '20',
        goProj_capacity        =>  '20',
        geneCoverage_capacity  =>  '100',

    ## Flag controling the use of the is_tree_compliant flag from the homology table of the Compara database
    ## If this flag is on (=1) then the pipeline will exclude all homologies where is_tree_compliant=0 in the homology table of the Compara db
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