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AnalyzeTables_conf.pm
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AnalyzeTables_conf.pm
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=head1 LICENSE
See the NOTICE file distributed with this work for additional information
regarding copyright ownership.
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::EGPipeline::PipeConfig::AnalyzeTables_conf
=head1 DESCRIPTION
Analyze (or optionally optimize) all tables in a database.
=cut
package Bio::EnsEMBL::EGPipeline::PipeConfig::AnalyzeTables_conf;
use strict;
use warnings;
use Bio::EnsEMBL::Hive::Version 2.3;
use base ('Bio::EnsEMBL::EGPipeline::PipeConfig::EGGeneric_conf');
sub default_options {
my ($self) = @_;
return {
%{$self->SUPER::default_options},
pipeline_name => 'analyze_tables_'.$self->o('ensembl_release'),
species => [],
division => [],
run_all => 0,
antispecies => [],
meta_filters => {},
optimize_tables => 0,
};
}
sub beekeeper_extra_cmdline_options {
my $self = shift;
return "-reg_conf ".$self->o("registry");
}
sub pipeline_analyses {
my ($self) = @_;
return [
{
-logic_name => 'SpeciesFactory',
-module => 'Bio::EnsEMBL::EGPipeline::Common::RunnableDB::EGSpeciesFactory',
-parameters => {
species => $self->o('species'),
division => $self->o('division'),
run_all => $self->o('run_all'),
antispecies => $self->o('antispecies'),
meta_filters => $self->o('meta_filters'),
core_flow => 2,
chromosome_flow => 0,
regulation_flow => 3,
variation_flow => 4,
},
-input_ids => [ {} ],
-max_retry_count => 1,
-flow_into => {
'2' => ['AnalyzeTablesCore', 'AnalyzeTablesOtherFeatures'],
'3' => ['AnalyzeTablesRegulation'],
'4' => ['AnalyzeTablesVariation'],
},
-meadow_type => 'LOCAL',
},
{
-logic_name => 'AnalyzeTablesCore',
-module => 'Bio::EnsEMBL::EGPipeline::Common::RunnableDB::AnalyzeTables',
-parameters => {
optimize_tables => $self->o('optimize_tables'),
db_types => ['core'],
},
-max_retry_count => 1,
-analysis_capacity => 10,
-rc_name => 'normal',
},
{
-logic_name => 'AnalyzeTablesOtherFeatures',
-module => 'Bio::EnsEMBL::EGPipeline::Common::RunnableDB::AnalyzeTables',
-parameters => {
optimize_tables => $self->o('optimize_tables'),
db_types => ['otherfeatures'],
},
-max_retry_count => 1,
-analysis_capacity => 10,
-rc_name => 'normal',
},
{
-logic_name => 'AnalyzeTablesRegulation',
-module => 'Bio::EnsEMBL::EGPipeline::Common::RunnableDB::AnalyzeTables',
-parameters => {
optimize_tables => $self->o('optimize_tables'),
db_types => ['funcgen'],
},
-max_retry_count => 1,
-analysis_capacity => 10,
-rc_name => 'normal',
},
{
-logic_name => 'AnalyzeTablesVariation',
-module => 'Bio::EnsEMBL::EGPipeline::Common::RunnableDB::AnalyzeTables',
-parameters => {
optimize_tables => $self->o('optimize_tables'),
db_types => ['variation'],
},
-max_retry_count => 1,
-analysis_capacity => 10,
-rc_name => 'normal',
},
];
}
1;