RunListOfCommandsOnFarm_conf.pm

Go to the documentation of this file.

=pod
 
=head1 NAME
 
    Bio::EnsEMBL::Hive::Examples::Factories::PipeConfig::RunListOfCommandsOnFarm_conf
 
=head1 SYNOPSIS
 
    init_pipeline.pl Bio::EnsEMBL::Hive::Examples::Factories::PipeConfig::RunListOfCommandsOnFarm_conf -password <your_password> -inputfile file_with_cmds.txt
 
=head1 DESCRIPTION
 
    This is an example pipeline put together from basic building blocks:
 
    Analysis_1: JobFactory.pm is used to turn the list of commands in a file into jobs
 
        these jobs are sent down the branch #2 into the second analysis
 
    Analysis_2: SystemCmd.pm is used to run these jobs in parallel.
 
=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::RunListOfCommandsOnFarm_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
 
=head2 default_options
 
    Description : Implements default_options() interface method of Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf that is used to initialize default options.
                  In addition to the standard things it defines three options:
                    o('capacity')   defines how many files can be run in parallel
                
                  There are rules dependent on two options that do not have defaults (this makes them mandatory):
                    o('password')           your read-write password for creation and maintenance of the hive database
                    o('inputfile')          name of the inputfile where the commands are
 
=cut
 
sub default_options {
    my ($self) = @_;
    return {
        %{ $self->SUPER::default_options() },               # inherit other stuff from the base class
 
        'pipeline_name' => 'ifile_syscmd',                  # name used by the beekeeper to prefix job names on the farm
 
        'capacity'  => 100,                                 # how many commands can be run in parallel
    };
}
 
 
=head2 pipeline_analyses
 
    Description : Implements pipeline_analyses() interface method of Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf that defines the structure of the pipeline: analyses, jobs, rules, etc.
                  Here it defines two analyses:
 
                    * 'create_jobs'  reads commands line-by-line from inputfile
                      Each job of this analysis will dataflow (create jobs) via branch #2 into 'run_cmd' analysis.
 
                    * 'run_cmd'   actually runs the commands in parallel
 
=cut
 
sub pipeline_analyses {
    my ($self) = @_;
    return [
        {   -logic_name => 'create_jobs',
            -module     => 'Bio::EnsEMBL::Hive::RunnableDB::JobFactory',
            -parameters => {
                'column_names' => [ 'cmd' ],
            },
            -input_ids => [
                { 'inputfile' => $self->o('inputfile') },   # A new file-with-commands could be loaded at each -topup_jobs execution of init_pipeline
            ],
            -flow_into => {
                2 => [ 'run_cmd' ],   # will create a fan of jobs
            },
        },
 
        {   -logic_name    => 'run_cmd',
            -module        => 'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd',
            -parameters    => { },
            -analysis_capacity => $self->o('capacity'),   # allow several workers to perform identical tasks in parallel
        },
    ];
}
 
1;