MiniPecanSingle_conf.pm 6.03 KB
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=pod

=head1 NAME

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    MiniPecanSingle_conf
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=head1 SYNOPSIS

    init_pipeline.pl MiniPecanSingle_conf -password <your_password>

    init_pipeline.pl MiniPecanSingle_conf -hive_driver sqlite -password <FOO>

=head1 DESCRIPTION

    This is an example pipeline put together from basic building blocks:

    Analysis_1: SystemCmd.pm is used to run Pecan on a set of files

        the job is sent down the branch #1 into the second analysis

    Analysis_2: SystemCmd.pm is used to run gerp_col on the resulting alignment

        the job is sent down the branch #1 into the third analysis

    Analysis_3: SystemCmd.pm is used to run gerp_elem on the GERP scores

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=head1 LICENSE

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    Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Matthieu Muffato's avatar
Matthieu Muffato committed
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    Copyright [2016-2018] EMBL-European Bioinformatics Institute
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    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.

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=head1 CONTACT

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    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
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=cut

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package MiniPecanSingle_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

=cut

sub default_options {
    my ($self) = @_;
    return {
        %{ $self->SUPER::default_options() },             # inherit other stuff from the base class

        'pipeline_name' => 'mini_pecan_single',           # name used by the beekeeper to prefix job names on the farm

    };
}


=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:

                    * 'pecan'  aligns sequences with Pecan
                      Each job of this analysis will dataflow (create jobs) via branch #1 into 'gerp_col' analysis.

                    * 'gerp_col' runs gerp_col on Pecan output
                      Each job of this analysis will dataflow (create jobs) via branch #1 into 'gerp_elem' analysis.

                    * 'gerp_elem' runs gerp_elem on gerp_col output

=cut

sub pipeline_analyses {
    my ($self) = @_;
    return [

        ## First analysis: PECAN
        {   -logic_name => 'pecan',
            -module     => 'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd',
            -parameters => {
                # The cmd parameter is required by the SystemCmd module. It defines the command line to be run.
                # Note that some values are written between #hashes#. Those will be subtituted by the corresponding input values
                'cmd'     => 'java -cp /soft/pecan_v0.8/pecan_v0.8.jar bp.pecan.Pecan -E "#tree_string#" -F #input_files# -G #msa_file#',
            },
            
            -input_ids  => [
                # Each input_id is a new job for this analysis. Here we are defining the input_files and the msa_file for
                # the first and only job.
                {
                  'tree_string' => '((((HUMAN,(MOUSE,RAT)),COW),OPOSSUM),CHICKEN);',
                  'input_files' => 'human.fa mouse.fa rat.fa cow.fa opossum.fa chicken.fa',
                  'msa_file'    => "pecan.mfa",
                },
            ],
            -flow_into => {
                # dataflow rule. Once a 'pecan' job is done, it will create a new 'gerp_col' job.
                # The input_id for the new job will be the same as for the previous job (this is
                # only true for branch 1. In this case, 'tree_string', 'input_files' and 'msa_file'
                # values are used to create a new 'gerp_col' job (only msa_file is actually required).
                1 => [ 'gerp_col' ],
            },
        },



        ## Second analysis: GERP_COL
        {   -logic_name => 'gerp_col',
            -module     => 'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd',
            -parameters => {
                # In this case, #msa_file# comes from the parent 'pecan' job.
                'cmd'         => 'gerpcol -t tree.nw -f #msa_file# -a -e HUMAN',
            },
            -flow_into => {
                # dataflow rule, branch 1. The input_id for the new job will be the same as for the
                # previous job, i.e. 'tree_string', 'input_files' and 'msa_file' values are used to
                # create a new 'gerp_elem' job (only msa_file is actually required).
                1 => [ 'gerp_elem' ],
            },
        },


        ## Third analysis: GERP_ELEM
        {   -logic_name => 'gerp_elem',
            -module     => 'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd',
            -parameters => {
                # In this case, #msa_file# comes from the parent 'gerp_col' job, which in turn comes from its parent 'pecan' job.
                'cmd'   => 'gerpelem -f #msa_file#.rates -c chr13 -s 32878016 -x .bed',
            },
        },

    ];
}


1;