files for running handover pipeline over EG databases

modules/Bio/EnsEMBL/Pipeline/PipeConfig/EG_misc_tasks_conf.pm

+package Bio::EnsEMBL::Pipeline::PipeConfig::EG_misc_tasks_conf;
+
+use strict;
+use warnings;
+
+use base ('Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf');
+
+use Bio::EnsEMBL::ApiVersion qw/software_version/;
+
+sub default_options {
+    my ($self) = @_;
+
+    return {
+        # inherit other stuff from the base class
+        %{ $self->SUPER::default_options() },
+
+        ### OVERRIDE
+
+        ### Optional overrides
+        species => [],
+
+        division => [],
+
+        release => software_version(),
+
+        run_all => 0,
+
+        bin_count => '150',
+
+        max_run => '100',
+
+        ### Defaults
+
+        pipeline_name => 'misc_tasks_'.$self->o('release'),
+
+        email => $self->o('ENV', 'USER').'@ebi.ac.uk',
+    };
+}
+
+sub pipeline_create_commands {
+    my ($self) = @_;
+    return [
+      # inheriting database and hive tables' creation
+      @{$self->SUPER::pipeline_create_commands},
+    ];
+}
+
+## See diagram for pipeline structure
+sub pipeline_analyses {
+    my ($self) = @_;
+
+    return [
+
+      {
+        -logic_name => 'ScheduleSpecies',
+        -module     => 'Bio::EnsEMBL::Pipeline::Production::EGSpeciesFactory',
+        -parameters => {
+          species => $self->o('species'),
+          division => $self->o('division'),
+          run_all => $self->o('run_all'),
+          max_run => $self->o('max_run')
+
+        },
+        -input_ids  => [ {} ],
+        -max_retry_count  => 1,
+        -flow_into  => {
+         '3->B' => ['PercentRepeat'],
+         'B->3' => ['PercentGC'],
+         '3->C' => ['CodingDensity'],
+         'C->3' => ['NonCodingDensity'],
+         '3->A' => ['PercentRepeat', 'CodingDensity', 'NonCodingDensity', 'PercentGC'],
+         '2->A' => ['GeneGC', 'GeneCount', 'ConstitutiveExons'], # Should inclued 'PepStats'
+         'A->1' => ['NotifyCore'],
+         '4->D' => ['SnpDensity', 'SnpCount'],
+         'D->1' => ['NotifyVariation'],
+        },
+      },
+
+      {
+        -logic_name => 'ConstitutiveExons',
+        -module     => 'Bio::EnsEMBL::Pipeline::Production::ConstitutiveExons',
+        -parameters => {
+          dbtype => 'core',
+        },
+        -max_retry_count  => 3,
+        -hive_capacity    => 100,
+        -rc_name          => 'normal',
+      },
+
+      {
+        -logic_name => 'PepStats',
+        -module     => 'Bio::EnsEMBL::Pipeline::Production::PepStats',
+        -parameters => {
+          tmpdir => '/tmp', binpath => '/nfs/panda/ensemblgenomes/external/EMBOSS',
+          dbtype => 'core',
+        },
+        -max_retry_count  => 3,
+        -hive_capacity    => 100,
+        -rc_name          => 'mem',
+      },
+
+      {
+        -logic_name => 'GeneCount',
+        -module     => 'Bio::EnsEMBL::Pipeline::Production::GeneCount',
+        -max_retry_count  => 3,
+        -hive_capacity    => 100,
+        -rc_name          => 'normal',
+      },
+
+      {
+        -logic_name => 'NonCodingDensity',
+        -module     => 'Bio::EnsEMBL::Pipeline::Production::NonCodingDensity',
+        -parameters => {
+          logic_name => 'noncodingdensity', value_type => 'sum',
+          bin_count => $self->o('bin_count'), max_run => $self->o('max_run'),
+        },
+        -max_retry_count  => 3,
+        -hive_capacity    => 100,
+        -rc_name          => 'normal',
+        -can_be_empty     => 1,
+        -flow_into => ['PseudogeneDensity'],
+      },
+
+      {
+        -logic_name => 'PseudogeneDensity',
+        -module     => 'Bio::EnsEMBL::Pipeline::Production::PseudogeneDensity',
+        -parameters => {
+          logic_name => 'pseudogenedensity', value_type => 'sum',
+          bin_count => $self->o('bin_count'), max_run => $self->o('max_run'),
+        },
+        -max_retry_count  => 3,
+        -hive_capacity    => 100,
+        -rc_name          => 'normal',
+        -can_be_empty     => 1,
+      },
+
+      {
+        -logic_name => 'CodingDensity',
+        -module     => 'Bio::EnsEMBL::Pipeline::Production::CodingDensity',
+        -parameters => {
+          logic_name => 'codingdensity', value_type => 'sum',
+          bin_count => $self->o('bin_count'), max_run => $self->o('max_run'),
+        },
+        -max_retry_count  => 3,
+        -hive_capacity    => 100,
+        -rc_name          => 'normal',
+        -can_be_empty     => 1,
+      },
+
+      {
+        -logic_name => 'GeneGC',
+        -module     => 'Bio::EnsEMBL::Pipeline::Production::GeneGC',
+        -max_retry_count  => 3,
+        -hive_capacity    => 100,
+        -rc_name => 'normal',
+      },
+
+      {
+        -logic_name => 'PercentGC',
+        -module     => 'Bio::EnsEMBL::Pipeline::Production::PercentGC',
+        -parameters => {
+          table => 'repeat', logic_name => 'percentgc', value_type => 'ratio',
+          bin_count => $self->o('bin_count'), max_run => $self->o('max_run'),
+        },
+        -max_retry_count  => 3,
+        -hive_capacity    => 100,
+        -rc_name          => 'normal',
+        -can_be_empty     => 1,
+      },
+
+      {
+        -logic_name => 'PercentRepeat',
+        -module     => 'Bio::EnsEMBL::Pipeline::Production::PercentRepeat',
+        -parameters => {
+          logic_name => 'percentagerepeat', value_type => 'ratio',
+          bin_count => $self->o('bin_count'), max_run => $self->o('max_run'),
+        },
+        -max_retry_count  => 3,
+        -hive_capacity    => 100,
+        -rc_name          => 'mem',
+        -can_be_empty     => 1,
+      },
+
+      {
+        -logic_name => 'SnpCount',
+        -module     => 'Bio::EnsEMBL::Pipeline::Production::SnpCount',
+        -max_retry_count  => 1,
+        -hive_capacity    => 10,
+        -rc_name          => 'normal',
+        -can_be_empty     => 1,
+      },
+
+      {
+        -logic_name => 'SnpDensity',
+        -module     => 'Bio::EnsEMBL::Pipeline::Production::SnpDensity',
+        -parameters => {
+          table => 'gene', logic_name => 'snpdensity', value_type => 'sum',
+          bin_count => $self->o('bin_count'), max_run => $self->o('max_run'),
+        },
+        -max_retry_count  => 1,
+        -hive_capacity    => 10,
+        -rc_name          => 'normal',
+        -can_be_empty     => 1,
+      },
+
+      ####### NOTIFICATION
+
+      {
+        -logic_name => 'NotifyCore',
+        -module     => 'Bio::EnsEMBL::Pipeline::Production::EmailSummaryCore',
+        -parameters => {
+          email   => $self->o('email'),
+          subject => $self->o('pipeline_name').' (core) has finished',
+        },
+      },
+
+      {
+        -logic_name => 'NotifyVariation',
+        -module     => 'Bio::EnsEMBL::Pipeline::Production::EmailSummaryVariation',
+        -parameters => {
+          email   => $self->o('email'),
+          subject => $self->o('pipeline_name').' (variation) has finished',
+        },
+      }
+
+    ];
+}
+
+sub pipeline_wide_parameters {
+    my ($self) = @_;
+
+    return {
+        %{ $self->SUPER::pipeline_wide_parameters() },  # inherit other stuff from the base class
+        release => $self->o('release'),
+        species => $self->o('species'),
+        species => $self->o('division'),
+    };
+}
+
+# override the default method, to force an automatic loading of the registry in all workers
+sub beekeeper_extra_cmdline_options {
+    my $self = shift;
+    return "-reg_conf ".$self->o("registry");
+}
+
+sub resource_classes {
+    my $self = shift;
+    return {
+      'default' => { 'LSF' => ''},
+      'normal'  => { 'LSF' => '-q production-rh6 -n 4 -M 4000 -R "rusage[mem=4000]"'},
+      'mem'     => { 'LSF' => '-q production-rh6 -n 4 -M 12000 -R "rusage[mem=12000]"'},
+    }
+}
+
+1;

modules/Bio/EnsEMBL/Pipeline/Production/EGSpeciesFactory.pm

+
+=pod
+
+=head1 LICENSE
+
+  Copyright (c) 1999-2012 The European Bioinformatics Institute and
+  Genome Research Limited.  All rights reserved.
+
+  This software is distributed under a modified Apache license.
+  For license details, please see
+
+    http://www.ensembl.org/info/about/code_licence.html
+
+=head1 CONTACT
+
+  Please email comments or questions to the public Ensembl
+  developers list at <dev@ensembl.org>.
+
+  Questions may also be sent to the Ensembl help desk at
+  <helpdesk@ensembl.org>.
+
+=head1 NAME
+
+Bio::EnsEMBL::Pipeline::Production::EGSpeciesFactory
+
+=head1 DESCRIPTION
+
+An extension of the ClassSpeciesFactory code, for use with
+EnsemblGenomes, which uses the production database differently
+and thus needs a simpler 'is_run' function.
+
+=cut
+
+package Bio::EnsEMBL::Pipeline::Production::EGSpeciesFactory;
+
+use strict;
+use warnings;
+
+use base qw/Bio::EnsEMBL::Pipeline::Production::ClassSpeciesFactory/;
+
+sub is_run {
+	my ( $self, $dba, $class ) = @_;
+	my $production_name = $dba->get_MetaContainer()->get_production_name();
+
+	if ( $class =~ 'karyotype' ) {
+		return $self->has_karyotype($dba);
+	}
+	$dba->dbc()->disconnect_if_idle();
+	return 1;
+}
+
+sub process_dba {
+	my ( $self, $dba ) = @_;
+	my $result = $self->SUPER::process_dba($dba);
+	if ( $result == 1 && @{ $self->param('division') } ) {
+		$result = 0;
+		for my $division (@{$self->param('division')}) {
+			if($dba->get_MetaContainer()->get_division() eq $division) {
+				$result = 1;
+				last;
+			}
+		}
+		$dba->dbc()->disconnect_if_idle();
+	}
+	return $result;
+}
+1;