LeachingTest_conf.pm

Go to the documentation of this file.

=pod
 
=head1 NAME
 
    Bio::EnsEMBL::Hive::Examples::Factories::PipeConfig::LeachingTest_conf
 
=head1 SYNOPSIS
 
    init_pipeline.pl Bio::EnsEMBL::Hive::Examples::Factories::PipeConfig::LeachingTest_conf -password <your_password>
 
=head1 DESCRIPTION
 
    When we attempt to create a new semaphored group of jobs and the creation of the funnel job fails
    because there is already a job with the same primary key, we reuse this funnel job and simply top up
    the semaphore group with extra fan jobs. This is what we call "leaching".
 
    This is a small pipeline to test leaching via using templates.
 
    Note 1: this is not the recommended way to create a single backbone from multiple independent streams!
 
    Note 2: the 'start' analysis is only needed because of the recently adopted rule of automatically param-stacking
            the very first job that does not have a local parent (used mainly for maintaining cross-database return capability,
            but could prove itself useful in other contexts as well). If/when we decide against this feature,
            we can also drop the 'start' analysis, leaving two independent seeding jobs in 'factory' analysis
            and changing the leeching.t test accordingly (removing one execution of runWorker).
 
=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.
 
=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::Examples::Factories::PipeConfig::LeachingTest_conf;
 
use strict;
use warnings;
 
use base ('Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf');  # All Hive databases configuration files should inherit from HiveGeneric, directly or indirectly
 
 
sub pipeline_analyses {
    my ($self) = @_;
    return [
        {   -logic_name => 'start',
            -module     => 'Bio::EnsEMBL::Hive::RunnableDB::Dummy',
            -input_ids => [
                {},
            ],
            -flow_into => {
                1 => {
                    'factory' => [ {'inputlist' => [ 11, 33, 55, 66, 77 ]}, {'inputlist' => [22, 44, 55, 66 ]} ],
                    'aggregator' => {},
                },
            },
        },
 
        {   -logic_name => 'factory',
            -module     => 'Bio::EnsEMBL::Hive::RunnableDB::JobFactory',
            -parameters => {
                'column_names' => [ 'alpha' ],
            },
            -flow_into => {                                         # There are two input jobs...
                '2->A'  => 'fan',
                'A->1'  => { 'funnel' => { 'funnel_id' => 7 }},     # ...however we want all of the children to report to one common funnel
            },
        },
 
        {   -logic_name    => 'fan',
            -module        => 'Bio::EnsEMBL::Hive::RunnableDB::Dummy',
            -flow_into => {
                1 => '?accu_name=alphas&accu_input_variable=alpha&accu_address=[]',
            },
        },
 
        {   -logic_name    => 'funnel',
            -module        => 'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd',
            -parameters => {
                'alpha_csv' => '#expr( join(",", @{#alphas#}) )expr#',
                'cmd'       => 'echo "#alpha_csv#"',
            },
            -flow_into => {
                '1->A' => 'fan',
                'A->1' => { 'aggregator' => {}, },
            },
        },
 
        {   -logic_name    => 'aggregator',
            -module        => 'Bio::EnsEMBL::Hive::RunnableDB::Dummy',
        },
    ];
}
 
1;