CompressFiles_conf.pm

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=pod
 
=head1 NAME
 
    Bio::EnsEMBL::Hive::Examples::Factories::PipeConfig::CompressFiles_conf
 
=head1 SYNOPSIS
 
    init_pipeline.pl Bio::EnsEMBL::Hive::Examples::Factories::PipeConfig::CompressFiles_conf -password <your_password>
 
    seed_pipeline.pl -url <url> -logic_name find_files -input_id "{ 'directory' => 'dumps' }"
 
=head1 DESCRIPTION
 
    This is an example pipeline put together from two basic building blocks:
 
    Analysis_1: JobFactory.pm is used to turn the list of files in a given directory into jobs
 
        these jobs are sent down the branch #2 into the second analysis
 
    Analysis_2: SystemCmd.pm is used to run these compression/decompression 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::CompressFiles_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 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:
 
                    * 'find_files'          generates a list of files whose names match the pattern #only_files#
                                            Each job of this analysis will dataflow (create jobs) via branch #2 into 'compress_a_file' analysis.
 
                    * 'compress_a_file'     actually performs the (un)gzipping of the files in parallel
 
=cut
 
sub pipeline_analyses {
    my ($self) = @_;
    return [
        {   -logic_name => 'find_files',
            -module     => 'Bio::EnsEMBL::Hive::RunnableDB::JobFactory',
            -parameters => {
                'inputcmd'     => 'find #directory# -type f',
                'column_names' => [ 'filename' ],
            },
            -flow_into => {
                2 => [ 'compress_a_file' ],     # will create a fan of jobs
            },
        },
 
        {   -logic_name    => 'compress_a_file',
            -module        => 'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd',
            -parameters    => {
                'cmd'       => 'gzip #filename#',
            },
            -analysis_capacity => 4,            # limit the number of workers that will be performing jobs in parallel
        },
    ];
}
 
1;