diff --git a/modules/Bio/EnsEMBL/Pipeline/PipeConfig/EG_misc_tasks_conf.pm b/modules/Bio/EnsEMBL/Pipeline/PipeConfig/EG_misc_tasks_conf.pm
new file mode 100644
index 0000000000000000000000000000000000000000..fc061eb716f0ec2736c4eec3e8f7decaad7cbd51
--- /dev/null
+++ b/modules/Bio/EnsEMBL/Pipeline/PipeConfig/EG_misc_tasks_conf.pm
@@ -0,0 +1,255 @@
+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;
diff --git a/modules/Bio/EnsEMBL/Pipeline/Production/EGSpeciesFactory.pm b/modules/Bio/EnsEMBL/Pipeline/Production/EGSpeciesFactory.pm
new file mode 100644
index 0000000000000000000000000000000000000000..b33f990b160cdea9de8b9d2127d4cb8c43d2d4f5
--- /dev/null
+++ b/modules/Bio/EnsEMBL/Pipeline/Production/EGSpeciesFactory.pm
@@ -0,0 +1,67 @@
+
+=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;