=head1 LICENSE Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2019] EMBL-European Bioinformatics Institute 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. =cut =head1 CONTACT Please email comments or questions to the public Ensembl developers list at . Questions may also be sent to the Ensembl help desk at . =head1 NAME Bio::EnsEMBL::Compara::PipeConfig::EPO_pt3_conf =head1 DESCRIPTION The PipeConfig file for the last part (3rd part) of the EPO pipeline. This will genereate the multiple sequence alignments (MSA) from a database containing a set of anchor sequences mapped to a set of target genomes. The pipeline runs Enredo (which generates a graph of the syntenic regions of the target genomes) and then runs Ortheus (which runs Pecan for generating the MSA) and infers ancestral genome sequences. Finally Gerp may be run to generate constrained elements and conservation scores from the MSA =head1 SYNOPSIS #1. update ensembl-hive, ensembl and ensembl-compara GIT repositories before each new release #3. make sure that all default_options are set correctly #4. Run init_pipeline.pl script: init_pipeline.pl Bio::EnsEMBL::Compara::PipeConfig::EPO_pt3_conf -password -mlss_id -species_set_name -compara_mapped_anchor_db -master_db <> #5. Sync and loop the beekeeper.pl as shown in init_pipeline.pl's output =head1 AUTHORSHIP Ensembl Team. Individual contributions can be found in the GIT log. =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with an underscore (_) =cut package Bio::EnsEMBL::Compara::PipeConfig::EPO_pt3_conf; use strict; use warnings; use Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf; # Allow this particular config to use conditional dataflow use Bio::EnsEMBL::Compara::PipeConfig::Parts::EPOAlignment; use Bio::EnsEMBL::Compara::PipeConfig::Parts::MultipleAlignerStats; use base ('Bio::EnsEMBL::Compara::PipeConfig::ComparaGeneric_conf'); sub default_options { my ($self) = @_; return { %{$self->SUPER::default_options}, 'pipeline_name' => $self->o('species_set_name').'_epo_'.$self->o('rel_with_suffix'), # 'mlss_id' => 647, # method_link_species_set_id of the ortheus alignments which will be generated 'run_gerp' => 0, 'enredo_params' => ' --min-score 0 --max-gap-length 200000 --max-path-dissimilarity 4 --min-length 10000 '. '--min-regions 2 --min-anchors 3 --max-ratio 3 --simplify-graph 7 --bridges -o ', # Dump directory 'enredo_output_file' => $self->o('dump_dir').'enredo_#mlss_id#.out', 'bed_dir' => $self->o('dump_dir').'bed_dir', 'output_dir' => $self->o('dump_dir').'feature_dumps', 'enredo_mapping_file' => $self->o('dump_dir').'enredo_friendly.mlssid_#mlss_id#_'.$self->o('rel_with_suffix'), 'bl2seq_dump_dir' => $self->o('dump_dir').'bl2seq', # location for dumping sequences to determine strand (for bl2seq) 'bl2seq_file_stem' => $self->o('bl2seq_dump_dir')."/bl2seq", # add MT dnafrags separately (1) or not (0) to the dnafrag_region table 'add_non_nuclear_alignments' => 1, 'gerp_window_sizes' => [1,10,100,500], #gerp window sizes 'skip_multiplealigner_stats' => 0, #skip this module if set to 1 'ancestral_sequences_name' => 'ancestral_sequences', }; } sub pipeline_create_commands { my ($self) = @_; return [ @{$self->SUPER::pipeline_create_commands}, $self->pipeline_create_commands_rm_mkdir(['dump_dir', 'bl2seq_dump_dir', 'output_dir', 'bed_dir']), ]; } sub pipeline_wide_parameters { my $self = shift @_; return { %{$self->SUPER::pipeline_wide_parameters}, 'ancestral_db' => $self->o('ancestral_db'), 'enredo_mapping_file' => $self->o('enredo_mapping_file'), 'master_db' => $self->o('master_db'), 'compara_mapped_anchor_db' => $self->o('compara_mapped_anchor_db'), 'mlss_id' => $self->o('mlss_id'), 'enredo_output_file' => $self->o('enredo_output_file'), 'run_gerp' => $self->o('run_gerp'), 'genome_dumps_dir' => $self->o('genome_dumps_dir'), }; } sub core_pipeline_analyses { my ($self) = @_; return [ { -logic_name => 'copy_table_factory', -module => 'Bio::EnsEMBL::Hive::RunnableDB::JobFactory', -parameters => { 'db_conn' => '#compara_mapped_anchor_db#', 'inputlist' => [ 'method_link', 'genome_db', 'species_set', 'species_set_header', 'method_link_species_set', 'dnafrag', 'ncbi_taxa_name', 'ncbi_taxa_node' ], 'column_names' => [ 'table' ], }, -input_ids => [{}], -flow_into => { '2->A' => { 'copy_table' => { 'src_db_conn' => '#db_conn#', 'table' => '#table#' } }, '1->A' => [ 'drop_ancestral_db', 'set_internal_ids' ], 'A->1' => [ 'copy_mlss' ], }, }, { -logic_name => 'copy_table', -module => 'Bio::EnsEMBL::Hive::RunnableDB::MySQLTransfer', -parameters => { 'mode' => 'topup', 'filter_cmd' => 'sed "s/ENGINE=MyISAM/ENGINE=InnoDB/"', }, }, { -logic_name => 'copy_mlss', -module => 'Bio::EnsEMBL::Hive::RunnableDB::MySQLTransfer', -parameters => { 'src_db_conn' => '#master_db#', 'mode' => 'topup', 'table' => 'method_link_species_set', 'where' => 'method_link_species_set_id = #mlss_id#', }, -flow_into => [ 'make_species_tree' ], }, @{ Bio::EnsEMBL::Compara::PipeConfig::Parts::EPOAlignment::pipeline_analyses_epo_alignment($self) }, ]; } sub tweak_analyses { my $self = shift; my $analyses_by_name = shift; $analyses_by_name->{'dump_mappings_to_file'}->{'-parameters'}->{'db_conn'} = '#compara_mapped_anchor_db#'; } 1;