=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::ncRNAtrees_conf =head1 SYNOPSIS init_pipeline.pl Bio::EnsEMBL::Compara::PipeConfig::ncRNAtrees_conf -password -mlss_id =head1 DESCRIPTION This is the Ensembl PipeConfig for the ncRNAtree pipeline. An example of use can be found in the Example folder. =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::ncRNAtrees_conf ; use strict; use warnings; use Bio::EnsEMBL::Hive::Version 2.4; use Bio::EnsEMBL::Compara::PipeConfig::Parts::CAFE; use Bio::EnsEMBL::Compara::PipeConfig::Parts::GeneMemberHomologyStats; use Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf; # For WHEN and INPUT_PLUS use base ('Bio::EnsEMBL::Compara::PipeConfig::ComparaGeneric_conf'); sub default_options { my ($self) = @_; return { %{$self->SUPER::default_options}, # User details #'email' => 'john.smith@example.com', # dependent parameters ('work_dir' should be defined) 'dump_dir' => $self->o('work_dir') . '/dumps', 'ss_picts_dir' => $self->o('work_dir') . '/ss_picts/', # How will the pipeline create clusters (families) ? # Possible values: 'rfam' (default) or 'ortholog' # 'blastp' means that the pipeline will clusters genes according to their RFAM accession # 'ortholog' means that the pipeline will use previously inferred orthologs to perform a cluster projection 'clustering_mode' => 'rfam', # Parameters to allow merging different runs of the pipeline 'dbID_range_index' => 14, 'label_prefix' => undef, # How much the pipeline will try to reuse from "prev_rel_db" # tree break 'treebreak_tags_to_copy' => ['model_id', 'model_name'], # misc parameters 'species_tree_input_file' => '', # empty value means 'create using genome_db+ncbi_taxonomy information'; can be overriden by a file with a tree in it 'binary_species_tree_input_file' => undef, # you can define your own species_tree for 'CAFE'. It *has* to be binary 'skip_epo' => 0, # Never tried this one. It may fail 'create_ss_picts' => 0, # ambiguity codes 'allow_ambiguity_codes' => 1, # Do we want to initialise the CAFE part now ? 'initialise_cafe_pipeline' => undef, # Data needed for CAFE 'cafe_lambdas' => '', # For now, we don't supply lambdas 'cafe_struct_tree_str' => '', # Not set by default 'full_species_tree_label' => 'full_species_tree', 'per_family_table' => 0, 'cafe_species' => [], # Ortholog-clustering parameters 'ref_ortholog_db' => undef, # Analyses usually don't fail 'hive_default_max_retry_count' => 1, }; } sub pipeline_create_commands { my ($self) = @_; return [ @{$self->SUPER::pipeline_create_commands}, # here we inherit creation of database, hive tables and compara tables $self->pipeline_create_commands_rm_mkdir(['work_dir', 'dump_dir', 'ss_picts_dir']), ]; } sub pipeline_wide_parameters { # these parameter values are visible to all analyses, can be overridden by parameters{} and input_id{} my ($self) = @_; return { %{$self->SUPER::pipeline_wide_parameters}, # here we inherit anything from the base class 'mlss_id' => $self->o('mlss_id'), 'master_db' => $self->o('master_db'), 'member_db' => $self->o('member_db'), 'prev_rel_db' => $self->o('prev_rel_db'), 'skip_epo' => $self->o('skip_epo'), 'epo_db' => $self->o('epo_db'), 'create_ss_picts' => $self->o('create_ss_picts'), 'initialise_cafe_pipeline' => $self->o('initialise_cafe_pipeline'), 'dbID_range_index' => $self->o('dbID_range_index'), 'clustering_mode' => $self->o('clustering_mode'), } } sub resource_classes { my ($self) = @_; return { %{$self->SUPER::resource_classes('include_multi_threaded')}, # inherit the standard resource classes, incl. multi-threaded }; } sub core_pipeline_analyses { my ($self) = @_; my %hc_params = ( -analysis_capacity => $self->o('hc_capacity'), -priority => $self->o('hc_priority'), -batch_size => $self->o('hc_batch_size'), ); my %raxml_parameters = ( 'raxml_pthread_exe_sse3' => $self->o('raxml_pthread_exe_sse3'), 'raxml_pthread_exe_avx' => $self->o('raxml_pthread_exe_avx'), 'raxml_exe_sse3' => $self->o('raxml_exe_sse3'), 'raxml_exe_avx' => $self->o('raxml_exe_avx'), ); my %examl_parameters = ( 'examl_exe_sse3' => $self->o('examl_exe_sse3'), 'examl_exe_avx' => $self->o('examl_exe_avx'), 'parse_examl_exe' => $self->o('parse_examl_exe'), 'mpirun_exe' => $self->o('mpirun_exe'), ); my %decision_analysis_params = ( -analysis_capacity => $self->o('decision_capacity'), -priority => $self->o('hc_priority'), -batch_size => 20, ); return [ # --------------------------------------------- [ backbone ]----------------------------------------------------------------------------- { -logic_name => 'backbone_fire_load_genomes', -module => 'Bio::EnsEMBL::Hive::RunnableDB::Dummy', -input_ids => [ {} ], -flow_into => { '1->A' => [ 'copy_tables_factory' ], 'A->1' => [ 'backbone_fire_classify_genes' ], }, -meadow_type=> 'LOCAL', }, { -logic_name => 'backbone_fire_classify_genes', -module => 'Bio::EnsEMBL::Hive::RunnableDB::DatabaseDumper', -parameters => { 'output_file' => $self->o('dump_dir').'/snapshot_before_classify.sql', }, -flow_into => { '1->A' => [ 'load_rfam_models' ], 'A->1' => [ 'backbone_fire_tree_building' ], }, }, { -logic_name => 'backbone_fire_tree_building', -module => 'Bio::EnsEMBL::Hive::RunnableDB::DatabaseDumper', -parameters => { 'output_file' => $self->o('dump_dir').'/snapshot_before_tree_building.sql', }, -flow_into => { '1->A' => [ 'clusters_factory' ], 'A->1' => [ 'backbone_pipeline_finished' ], }, }, { -logic_name => 'backbone_pipeline_finished', -module => 'Bio::EnsEMBL::Hive::RunnableDB::Dummy', -flow_into => ['notify_pipeline_completed'], -meadow_type=> 'LOCAL', }, { -logic_name => 'notify_pipeline_completed', -module => 'Bio::EnsEMBL::Compara::RunnableDB::NotifyByEmail', -parameters => { 'text' => 'The pipeline has completed.', 'email' => $self->o('email'), }, -flow_into => [ 'register_pipeline_url' ], }, { -logic_name => 'register_pipeline_url', -module => 'Bio::EnsEMBL::Compara::RunnableDB::RegisterMLSS', -parameters => { 'test_mode' => $self->o('test_mode'), } }, # ---------------------------------------------[copy tables from master and fix the offsets]--------------------------------------------- { -logic_name => 'copy_tables_factory', -module => 'Bio::EnsEMBL::Hive::RunnableDB::JobFactory', -parameters => { 'inputlist' => [ 'ncbi_taxa_node', 'ncbi_taxa_name', 'method_link' ], 'column_names' => [ 'table' ], }, -flow_into => { '2->A' => [ 'copy_table' ], 'A->1' => [ 'offset_tables' ], }, }, { -logic_name => 'copy_table', -module => 'Bio::EnsEMBL::Hive::RunnableDB::MySQLTransfer', -parameters => { 'src_db_conn' => '#master_db#', 'mode' => 'overwrite', 'filter_cmd' => 'sed "s/ENGINE=MyISAM/ENGINE=InnoDB/"', }, }, { -logic_name => 'offset_tables', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::OffsetTables', -parameters => { 'range_index' => '#dbID_range_index#', }, -flow_into => [ 'offset_more_tables' ], }, # CreateReuseSpeciesSets/PrepareSpeciesSetsMLSS may want to create new # entries. We need to make sure they don't collide with the master database { -logic_name => 'offset_more_tables', -module => 'Bio::EnsEMBL::Hive::RunnableDB::SqlCmd', -parameters => { 'sql' => [ 'ALTER TABLE species_set_header AUTO_INCREMENT=10000001', 'ALTER TABLE method_link_species_set AUTO_INCREMENT=10000001', ], }, -flow_into => [ 'load_genomedb_factory' ], }, # ---------------------------------------------[load GenomeDB entries from master+cores]--------------------------------------------- { -logic_name => 'load_genomedb_factory', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GenomeDBFactory', -parameters => { 'compara_db' => '#master_db#', # that's where genome_db_ids come from 'mlss_id' => $self->o('mlss_id'), 'extra_parameters' => [ 'locator' ], }, -flow_into => { '2->A' => { 'load_genomedb' => { 'master_dbID' => '#genome_db_id#', 'locator' => '#locator#' }, }, # fan 'A->1' => [ 'create_mlss_ss' ], }, }, { -logic_name => 'load_genomedb', -module => 'Bio::EnsEMBL::Compara::RunnableDB::LoadOneGenomeDB', -analysis_capacity => 10, }, { -logic_name => 'create_mlss_ss', -module => 'Bio::EnsEMBL::Compara::RunnableDB::PrepareSpeciesSetsMLSS', -parameters => { 'whole_method_links' => [ 'NC_TREES' ], 'singleton_method_links' => [ 'ENSEMBL_PARALOGUES', 'ENSEMBL_HOMOEOLOGUES' ], 'pairwise_method_links' => [ 'ENSEMBL_ORTHOLOGUES' ], }, -flow_into => { 1 => [ 'make_species_tree', 'load_members_factory' ], }, }, { -logic_name => 'hc_members_per_genome', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::SqlHealthChecks', -parameters => { mode => 'members_per_genome', allow_missing_coordinates => 0, allow_missing_cds_seqs => 0, allow_ambiguity_codes => $self->o('allow_ambiguity_codes'), only_canonical => 1, }, %hc_params, }, { -logic_name => 'load_members_factory', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GenomeDBFactory', -flow_into => { '2->A' => 'genome_member_copy', 'A->1' => [ 'hc_members_globally' ], }, }, { -logic_name => 'genome_member_copy', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::CopyCanonRefMembersByGenomeDB', -parameters => { 'reuse_db' => '#member_db#', 'biotype_filter' => 'biotype_group LIKE "%noncoding"', }, -analysis_capacity => 10, -flow_into => [ 'hc_members_per_genome' ], }, { -logic_name => 'hc_members_globally', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::SqlHealthChecks', -parameters => { mode => 'members_globally', }, -flow_into => [ 'insert_member_projections' ], %hc_params, }, { -logic_name => 'insert_member_projections', -module => 'Bio::EnsEMBL::Compara::RunnableDB::InsertMemberProjections', -parameters => { 'source_species_names' => [ 'homo_sapiens', 'mus_musculus', ], }, }, # ---------------------------------------------[load species tree]------------------------------------------------------------------- { -logic_name => 'make_species_tree', -module => 'Bio::EnsEMBL::Compara::RunnableDB::MakeSpeciesTree', -parameters => { 'species_tree_input_file' => $self->o('species_tree_input_file'), # empty by default, but if nonempty this file will be used instead of tree generation from genome_db 'multifurcation_deletes_all_subnodes' => [ 9347, 186625, 32561 ], }, -flow_into => { 2 => [ 'hc_species_tree' ], } }, { -logic_name => 'hc_species_tree', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::SqlHealthChecks', -parameters => { mode => 'species_tree', binary => 0, n_missing_species_in_tree => 0, }, %hc_params, }, # ---------------------------------------------[load RFAM models]--------------------------------------------------------------------- { -logic_name => 'load_rfam_models', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ComparaHMM::LoadInfernalHMMModels', -parameters => { 'url' => $self->o('rfam_ftp_url'), 'remote_file' => $self->o('rfam_remote_file'), 'expanded_basename' => $self->o('rfam_expanded_basename'), 'expander' => $self->o('rfam_expander'), 'type' => 'infernal', 'skip_consensus' => 1, }, -flow_into => WHEN( '#clustering_mode# eq "ortholog"' => 'ortholog_cluster', ELSE 'rfam_classify', ), }, # ---------------------------------------------[run RFAM classification]-------------------------------------------------------------- { -logic_name => 'rfam_classify', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::RFAMClassify', -parameters => { 'mirbase_url' => $self->o('mirbase_url'), }, -flow_into => [ 'expand_clusters_with_projections' ], -rc_name => '2Gb_job', }, { -logic_name => 'clusterset_backup', -module => 'Bio::EnsEMBL::Hive::RunnableDB::SqlCmd', -parameters => { 'sql' => 'INSERT IGNORE INTO gene_tree_backup (seq_member_id, root_id) SELECT seq_member_id, root_id FROM gene_tree_node WHERE seq_member_id IS NOT NULL', }, -flow_into => [ 'create_additional_clustersets' ], }, { -logic_name => 'create_additional_clustersets', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::CreateClustersets', -parameters => { 'member_type' => 'ncrna', 'additional_clustersets' => [qw(pg_it_nj ml_it_10 pg_it_phyml ss_it_s16 ss_it_s6a ss_it_s16a ss_it_s6b ss_it_s16b ss_it_s6c ss_it_s6d ss_it_s6e ss_it_s7a ss_it_s7b ss_it_s7c ss_it_s7d ss_it_s7e ss_it_s7f ft_it_ml ft_it_nj ftga_it_ml ftga_it_nj)], }, }, { -logic_name => 'cluster_qc_factory', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GenomeDBFactory', -flow_into => { '2->A' => [ 'per_genome_qc' ], 'A->1' => [ 'clusterset_backup' ], }, }, { -logic_name => 'per_genome_qc', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::PerGenomeGroupsetQC', }, { -logic_name => 'ortholog_cluster', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthologClusters', -parameters => { 'sort_clusters' => 1, 'add_model_id' => 1, }, -rc_name => '2Gb_job', -flow_into => 'expand_clusters_with_projections', }, { -logic_name => 'expand_clusters_with_projections', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::ExpandClustersWithProjections', -flow_into => [ 'cluster_qc_factory' ], -rc_name => '500Mb_job', }, # -------------------------------------------------[build trees]------------------------------------------------------------------ { -logic_name => 'clusters_factory', -module => 'Bio::EnsEMBL::Hive::RunnableDB::JobFactory', -parameters => { 'inputquery' => 'SELECT root_id AS gene_tree_id FROM gene_tree_root JOIN gene_tree_node USING (root_id) WHERE tree_type = "tree" GROUP BY root_id ORDER BY COUNT(*) DESC, root_id ASC', }, -flow_into => { '2->A' => WHEN( '#skip_epo#' => 'msa_chooser', ELSE 'recover_epo' ), 'A->1' => [ 'hc_global_tree_set' ], }, }, { -logic_name => 'hc_global_tree_set', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::SqlHealthChecks', -parameters => { mode => 'global_tree_set', }, -flow_into => [ 'write_stn_tags', WHEN('#clustering_mode# eq "ortholog"' => 'remove_overlapping_homologies', ELSE [ 'homology_stats_factory', 'id_map_mlss_factory' ]), WHEN('#initialise_cafe_pipeline# and #binary_species_tree_input_file#', 'CAFE_species_tree'), WHEN('#initialise_cafe_pipeline# and !#binary_species_tree_input_file#', 'make_full_species_tree'), ], %hc_params, }, { -logic_name => 'remove_overlapping_homologies', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::RemoveOverlappingHomologies', -flow_into => [ 'rename_labels' ], }, { -logic_name => 'rename_labels', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::RenameLabelsBeforMerge', -parameters => { 'clusterset_id'=> $self->o('collection'), 'label_prefix' => $self->o('label_prefix'), }, -flow_into => [ 'homology_stats_factory', 'id_map_mlss_factory' ], }, { -logic_name => 'write_stn_tags', -module => 'Bio::EnsEMBL::Hive::RunnableDB::DbCmd', -parameters => { 'input_file' => $self->o('tree_stats_sql'), }, -flow_into => [ 'email_tree_stats_report' ], }, { -logic_name => 'email_tree_stats_report', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::HTMLReport', -parameters => { 'email' => $self->o('email'), }, }, { -logic_name => 'recover_epo', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCRecoverEPO', -parameters => { 'max_members' => 50000, }, -analysis_capacity => $self->o('recover_capacity'), -flow_into => { 1 => 'hc_epo_removed_members', -1 => 'recover_epo_himem', }, -rc_name => '2Gb_job', }, { -logic_name => 'recover_epo_himem', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCRecoverEPO', -analysis_capacity => $self->o('recover_capacity'), -flow_into => [ 'hc_epo_removed_members' ], -rc_name => '16Gb_job', }, { -logic_name => 'hc_epo_removed_members', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::SqlHealthChecks', -parameters => { mode => 'epo_removed_members', }, -flow_into => [ 'msa_chooser' ], %hc_params, }, { -logic_name => 'msa_chooser', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::LoadTags', -parameters => { 'treebreak_gene_count' => $self->o('treebreak_gene_count'), 'tags' => { 'gene_count' => 0, }, }, -batch_size => 10, -rc_name => '1Gb_job', -priority => 30, -analysis_capacity => $self->o('msa_chooser_capacity'), -flow_into => WHEN( '#tree_gene_count# > #treebreak_gene_count#' => 'aligner_for_tree_break', ELSE 'tree_entry_point' ), }, { -logic_name => 'aligner_for_tree_break', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::Infernal', -analysis_capacity => $self->o('aligner_for_tree_break_capacity'), -parameters => { 'cmbuild_exe' => $self->o('cmbuild_exe'), 'cmalign_exe' => $self->o('cmalign_exe'), 'infernal_mxsize' => $self->o('infernal_mxsize'), }, -flow_into => { 1 => ['quick_tree_break' ], -1 => [ 'aligner_for_tree_break_himem' ], }, -rc_name => '2Gb_job', }, { -logic_name => 'aligner_for_tree_break_himem', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::Infernal', -analysis_capacity => $self->o('aligner_for_tree_break_capacity'), -parameters => { 'cmbuild_exe' => $self->o('cmbuild_exe'), 'cmalign_exe' => $self->o('cmalign_exe'), 'infernal_mxsize' => $self->o('infernal_mxsize'), }, -flow_into => [ 'quick_tree_break' ], -rc_name => '4Gb_job', }, { -logic_name => 'quick_tree_break', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::QuickTreeBreak', -parameters => { 'quicktree_exe' => $self->o('quicktree_exe'), 'tags_to_copy' => $self->o('treebreak_tags_to_copy'), 'treebreak_gene_count' => $self->o('treebreak_gene_count'), }, -analysis_capacity => $self->o('quick_tree_break_capacity'), -rc_name => '2Gb_job', -priority => 50, -flow_into => { 1 => ['other_paralogs'], -1 => ['quick_tree_break_himem'], # MEMLIMIT }, }, { -logic_name => 'quick_tree_break_himem', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::QuickTreeBreak', -parameters => { 'quicktree_exe' => $self->o('quicktree_exe'), 'tags_to_copy' => $self->o('treebreak_tags_to_copy'), 'treebreak_gene_count' => $self->o('treebreak_gene_count'), }, -analysis_capacity => $self->o('quick_tree_break_capacity'), -rc_name => '4Gb_job', -priority => 50, -flow_into => [ 'other_paralogs' ], }, { -logic_name => 'other_paralogs', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::OtherParalogs', -parameters => { 'dataflow_subclusters' => 1, }, -analysis_capacity => $self->o('other_paralogs_capacity'), -priority => 40, -rc_name => '1Gb_job', -flow_into => { -1 => [ 'other_paralogs_himem' ], 2 => [ 'tree_backup' ], 3 => { 'other_paralogs' => INPUT_PLUS }, }, }, { -logic_name => 'other_paralogs_himem', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::OtherParalogs', -parameters => { 'dataflow_subclusters' => 1, }, -analysis_capacity => $self->o('other_paralogs_capacity'), -priority => 40, -rc_name => '4Gb_job', -flow_into => { 2 => [ 'tree_backup' ], 3 => { 'other_paralogs_himem' => INPUT_PLUS }, }, }, { -logic_name => 'infernal', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::Infernal', -analysis_capacity => $self->o('infernal_capacity'), -parameters => { 'cmbuild_exe' => $self->o('cmbuild_exe'), 'cmalign_exe' => $self->o('cmalign_exe'), 'infernal_mxsize' => $self->o('infernal_mxsize'), }, -flow_into => { -1 => [ 'infernal_himem' ], 1 => [ 'secondary_structure_decision', WHEN('#create_ss_picts#' => 'create_ss_picts' ) ], }, -rc_name => '1Gb_job', }, { -logic_name => 'infernal_himem', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::Infernal', -analysis_capacity => $self->o('infernal_capacity'), -parameters => { 'cmbuild_exe' => $self->o('cmbuild_exe'), 'cmalign_exe' => $self->o('cmalign_exe'), 'infernal_mxsize' => $self->o('infernal_mxsize'), }, -flow_into => [ 'secondary_structure_decision', WHEN('#create_ss_picts#' => 'create_ss_picts' ) ], -rc_name => '16Gb_job', }, { -logic_name => 'secondary_structure_decision', -module => 'Bio::EnsEMBL::Hive::RunnableDB::Dummy', -flow_into => { 1 => WHEN( '(#aln_length# <= 200)' => 'pre_sec_struct_tree_1_core', '( (#aln_length# > 200) && (#aln_length# <= 600) )' => 'pre_sec_struct_tree_2_cores', '( (#aln_length# > 600) && (#aln_length# <= 1300) )' => 'pre_sec_struct_tree_4_cores', '(#aln_length# > 1300)' => 'pre_sec_struct_tree_8_cores', #'( #aln_length# > 4000 )' => 'pre_sec_struct_tree_16_cores', #Right now it may be an overkill, but it may be necessary in the future. ), }, %decision_analysis_params, }, { -logic_name => 'tree_backup', -module => 'Bio::EnsEMBL::Hive::RunnableDB::SqlCmd', -parameters => { 'sql' => 'INSERT INTO gene_tree_backup (seq_member_id, root_id) SELECT seq_member_id, root_id FROM gene_tree_node WHERE seq_member_id IS NOT NULL AND root_id = #gene_tree_id#', }, -flow_into => [ 'tree_entry_point' ], -analysis_capacity => 1, }, { -logic_name => 'tree_entry_point', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::LoadTags', -parameters => { 'tags' => { 'model_id' => '', }, }, -flow_into => { '1->A' => [ 'genomic_alignment', WHEN('#tree_model_id#' => 'infernal') ], 'A->1' => [ 'treebest_mmerge' ], }, }, { -logic_name => 'create_ss_picts', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::GenerateSSPict', -analysis_capacity => $self->o('ss_picts_capacity'), -parameters => { 'ss_picts_dir' => $self->o('ss_picts_dir'), 'r2r_exe' => $self->o('r2r_exe'), }, -rc_name => '2Gb_job', }, { -logic_name => 'pre_sec_struct_tree_1_core', ## pre_sec_struct_tree -module => 'Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::PrepareSecStructModels', ## PrepareRAxMLSecModels -- rename -analysis_capacity => $self->o('raxml_capacity'), -parameters => { %raxml_parameters, 'raxml_number_of_cores' => 1, 'more_cores_branch' => 3, 'cmd_max_runtime' => '43200', }, -flow_into => { -1 => [ 'pre_sec_struct_tree_2_cores' ], # This analysis also has more memory 2 => [ 'sec_struct_model_tree_1_core' ], 3 => [ 'pre_sec_struct_tree_2_cores' ], #After trying to restart RAxML we should escalate the capacity. }, }, { -logic_name => 'pre_sec_struct_tree_2_cores', ## pre_sec_struct_tree -module => 'Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::PrepareSecStructModels', ## PrepareRAxMLSecModels -- rename -analysis_capacity => $self->o('raxml_capacity'), -parameters => { %raxml_parameters, 'raxml_number_of_cores' => 2, 'more_cores_branch' => 3, 'cmd_max_runtime' => '43200', }, -flow_into => { -1 => [ 'pre_sec_struct_tree_4_cores' ], # This analysis also has more memory 2 => [ 'sec_struct_model_tree_2_cores' ], 3 => [ 'pre_sec_struct_tree_4_cores' ], }, -rc_name => '500Mb_2c_job', }, { -logic_name => 'pre_sec_struct_tree_4_cores', ## pre_sec_struct_tree -module => 'Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::PrepareSecStructModels', ## PrepareRAxMLSecModels -- rename -analysis_capacity => $self->o('raxml_capacity'), -parameters => { %raxml_parameters, 'raxml_number_of_cores' => 4, 'more_cores_branch' => 3, 'cmd_max_runtime' => '43200', }, -flow_into => { -1 => [ 'pre_sec_struct_tree_8_cores' ], # This analysis also has more memory 2 => [ 'sec_struct_model_tree_4_cores' ], 3 => [ 'pre_sec_struct_tree_8_cores' ], }, -rc_name => '1Gb_4c_job', }, { -logic_name => 'pre_sec_struct_tree_8_cores', ## pre_sec_struct_tree -module => 'Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::PrepareSecStructModels', ## PrepareRAxMLSecModels -- rename -analysis_capacity => $self->o('raxml_capacity'), -parameters => { %raxml_parameters, 'raxml_number_of_cores' => 8, }, -flow_into => { 2 => [ 'sec_struct_model_tree_8_cores' ], }, -rc_name => '2Gb_8c_job', }, { -logic_name => 'sec_struct_model_tree_1_core', ## sec_struct_model_tree -module => 'Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::SecStructModelTree', ## SecStrucModels -analysis_capacity => $self->o('raxml_capacity'), -parameters => { %raxml_parameters, 'raxml_number_of_cores' => 1, 'more_cores_branch' => 3, 'cmd_max_runtime' => '43200', }, -flow_into => { -1 => [ 'sec_struct_model_tree_2_cores' ], # This analysis has more cores *and* more memory 3 => [ 'sec_struct_model_tree_2_cores' ], }, }, { -logic_name => 'sec_struct_model_tree_2_cores', ## sec_struct_model_tree -module => 'Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::SecStructModelTree', ## SecStrucModels -analysis_capacity => $self->o('raxml_capacity'), -parameters => { %raxml_parameters, 'raxml_number_of_cores' => 2, 'more_cores_branch' => 3, 'cmd_max_runtime' => '43200', }, -flow_into => { -1 => [ 'sec_struct_model_tree_4_cores' ], # This analysis has more cores *and* more memory 3 => [ 'sec_struct_model_tree_4_cores' ], }, -rc_name => '500Mb_2c_job', }, { -logic_name => 'sec_struct_model_tree_4_cores', ## sec_struct_model_tree -module => 'Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::SecStructModelTree', ## SecStrucModels -analysis_capacity => $self->o('raxml_capacity'), -parameters => { %raxml_parameters, 'raxml_number_of_cores' => 4, 'more_cores_branch' => 3, 'cmd_max_runtime' => '43200', }, -flow_into => { -1 => [ 'sec_struct_model_tree_8_cores' ], # This analysis has more cores *and* more memory 3 => [ 'sec_struct_model_tree_8_cores' ], }, -rc_name => '1Gb_4c_job', }, { -logic_name => 'sec_struct_model_tree_8_cores', ## sec_struct_model_tree -module => 'Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::SecStructModelTree', ## SecStrucModels -analysis_capacity => $self->o('raxml_capacity'), -parameters => { %raxml_parameters, 'cmd_max_runtime' => '86400', 'raxml_number_of_cores' => 8, }, -rc_name => '2Gb_8c_job', }, { -logic_name => 'genomic_alignment', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCGenomicAlignment', -analysis_capacity => $self->o('genomic_alignment_capacity'), -parameters => { %raxml_parameters, 'cmd_max_runtime' => '43200', 'mafft_exe' => $self->o('mafft_exe'), 'raxml_number_of_cores' => 4, 'prank_exe' => $self->o('prank_exe'), 'genome_dumps_dir' => $self->o('genome_dumps_dir'), }, -flow_into => { -1 => ['genomic_alignment_himem'], 3 => ['fast_trees'], 2 => ['genomic_tree'], }, -rc_name => '2Gb_4c_job', -priority => $self->o('genomic_alignment_priority'), }, { -logic_name => 'fast_trees', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCFastTrees', -analysis_capacity => $self->o('fast_trees_capacity'), -parameters => { %examl_parameters, 'fasttree_exe' => $self->o('fasttree_exe'), 'parsimonator_exe' => $self->o('parsimonator_exe'), 'examl_number_of_cores' => 4, }, -flow_into => { -1 => ['fast_trees_himem'], }, -rc_name => '8Gb_4c_mpi', }, { -logic_name => 'fast_trees_himem', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCFastTrees', -analysis_capacity => $self->o('fast_trees_capacity'), -parameters => { %examl_parameters, 'fasttree_exe' => $self->o('fasttree_exe'), 'parsimonator_exe' => $self->o('parsimonator_exe'), 'examl_number_of_cores' => 4, }, -flow_into => { -1 => ['fast_trees_hugemem'], }, -rc_name => '16Gb_4c_mpi', }, { -logic_name => 'fast_trees_hugemem', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCFastTrees', -analysis_capacity => $self->o('fast_trees_capacity'), -parameters => { %examl_parameters, 'fasttree_exe' => $self->o('fasttree_exe'), 'parsimonator_exe' => $self->o('parsimonator_exe'), 'examl_number_of_cores' => 4, }, -rc_name => '32Gb_4c_mpi', }, { -logic_name => 'genomic_alignment_himem', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCGenomicAlignment', -analysis_capacity => $self->o('genomic_alignment_capacity'), -parameters => { %raxml_parameters, 'cmd_max_runtime' => '43200', 'raxml_number_of_cores' => 8, 'mafft_exe' => $self->o('mafft_exe'), 'prank_exe' => $self->o('prank_exe'), 'genome_dumps_dir' => $self->o('genome_dumps_dir'), 'inhugemem' => 1, }, -rc_name => '8Gb_8c_job', -priority => $self->o('genomic_alignment_himem_priority'), -flow_into => { 3 => [ 'fast_trees' ], 2 => [ 'genomic_tree_himem' ], -1 => [ 'genomic_alignment_hugemem' ], }, }, { -logic_name => 'genomic_alignment_hugemem', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCGenomicAlignment', -analysis_capacity => $self->o('genomic_alignment_capacity'), -parameters => { %raxml_parameters, 'raxml_number_of_cores' => 8, 'mafft_exe' => $self->o('mafft_exe'), 'prank_exe' => $self->o('prank_exe'), 'genome_dumps_dir' => $self->o('genome_dumps_dir'), 'inhugemem' => 1, }, -rc_name => '32Gb_8c_job', -flow_into => { 3 => [ 'fast_trees_himem' ], 2 => [ 'genomic_tree_himem' ], }, }, { -logic_name => 'genomic_tree', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCGenomicTree', -analysis_capacity => $self->o('genomic_tree_capacity'), -parameters => { 'treebest_exe' => $self->o('treebest_exe'), }, -flow_into => { -2 => ['genomic_tree_himem'], -1 => ['genomic_tree_himem'], }, }, { -logic_name => 'genomic_tree_himem', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCGenomicTree', -analysis_capacity => $self->o('genomic_tree_capacity'), -parameters => { 'treebest_exe' => $self->o('treebest_exe'), }, -rc_name => '1Gb_job', }, { -logic_name => 'treebest_mmerge', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCTreeBestMMerge', -analysis_capacity => $self->o('treebest_capacity'), -parameters => { 'treebest_exe' => $self->o('treebest_exe'), }, -flow_into => [ 'orthotree', 'ktreedist', 'consensus_cigar_line_prep' ], -rc_name => '1Gb_job', }, { -logic_name => 'orthotree', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::OrthoTree', -analysis_capacity => $self->o('orthotree_capacity'), -parameters => { 'tag_split_genes' => 0, }, -rc_name => '1Gb_job', -flow_into => { 1 => [ 'hc_tree_homologies' ], -1 => [ 'orthotree_himem' ], }, }, { -logic_name => 'orthotree_himem', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::OrthoTree', -analysis_capacity => $self->o('orthotree_capacity'), -parameters => { 'tag_split_genes' => 0, }, -flow_into => [ 'hc_tree_homologies' ], -rc_name => '4Gb_job', }, { -logic_name => 'ktreedist', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::Ktreedist', -parameters => { 'treebest_exe' => $self->o('treebest_exe'), 'ktreedist_exe' => $self->o('ktreedist_exe'), }, -rc_name => '1Gb_job', }, { -logic_name => 'consensus_cigar_line_prep', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ObjectStore::GeneTreeAlnConsensusCigarLine', -rc_name => '2Gb_job', -batch_size => 20, }, { -logic_name => 'hc_tree_homologies', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::SqlHealthChecks', -parameters => { mode => 'tree_homologies', }, -rc_name => '500Mb_job', %hc_params, }, { -logic_name => 'homology_stats_factory', -module => 'Bio::EnsEMBL::Compara::RunnableDB::MLSSIDFactory', -parameters => { 'methods' => { 'ENSEMBL_ORTHOLOGUES' => 2, 'ENSEMBL_PARALOGUES' => 3, }, }, -flow_into => { 1 => [ 'set_default_values' ], 2 => { 'orthology_stats' => { 'homo_mlss_id' => '#mlss_id#' }, }, 3 => { 'paralogy_stats' => { 'homo_mlss_id' => '#mlss_id#' }, }, }, }, { -logic_name => 'orthology_stats', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::OrthologyStats', -parameters => { 'member_type' => 'ncrna', }, -hive_capacity => $self->o('ortho_stats_capacity'), }, { -logic_name => 'paralogy_stats', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::ParalogyStats', -parameters => { 'member_type' => 'ncrna', }, -hive_capacity => $self->o('ortho_stats_capacity'), }, { -logic_name => 'id_map_mlss_factory', -module => 'Bio::EnsEMBL::Compara::RunnableDB::MLSSIDFactory', -parameters => { 'methods' => { 'ENSEMBL_ORTHOLOGUES' => 2, }, }, -flow_into => { 2 => [ 'mlss_id_mapping' ], }, }, { -logic_name => 'mlss_id_mapping', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::MLSSIDMapping', -hive_capacity => $self->o('homology_id_mapping_capacity'), -flow_into => { 1 => { 'homology_id_mapping' => INPUT_PLUS() } }, }, { -logic_name => 'homology_id_mapping', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::HomologyIDMapping', -flow_into => { -1 => [ 'homology_id_mapping_himem' ], }, -hive_capacity => $self->o('homology_id_mapping_capacity'), }, { -logic_name => 'homology_id_mapping_himem', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::HomologyIDMapping', -rc_name => '1Gb_job', -hive_capacity => $self->o('homology_id_mapping_capacity'), }, @{ Bio::EnsEMBL::Compara::PipeConfig::Parts::CAFE::pipeline_analyses_cafe_with_full_species_tree($self) }, @{ Bio::EnsEMBL::Compara::PipeConfig::Parts::GeneMemberHomologyStats::pipeline_analyses_hom_stats($self) }, ]; } 1;