=pod =head1 NAME Bio::EnsEMBL::Funcgen::PipeConfig::Segmentation =head1 SYNOPSIS =head1 DESCRIPTION =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. =head1 CONTACT =cut package Bio::EnsEMBL::Funcgen::PipeConfig::Segmentation; use strict; use warnings; use Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf; use base 'Bio::EnsEMBL::Funcgen::PipeConfig::PeakCalling::ResourceClasses'; #use base ('Bio::EnsEMBL::Funcgen::PipeConfig::PeakCalling::Base'); sub beekeeper_extra_cmdline_options { my ($self) = @_; return '-reg_conf ' . $self->o('reg_conf') . ' -keep_alive -can_respecialize 1'; } sub default_options { my ($self) = @_; return { %{ $self->SUPER::default_options() }, regulatory_build_name => 'The Ensembl regulatory build', regulatory_build_description => 'The Ensembl regulatory build', }; } sub pipeline_wide_parameters { my $self = shift; return { %{$self->SUPER::pipeline_wide_parameters}, pipeline_name => $self->o('pipeline_name'), tempdir => $self->o('tempdir'), tempdir_segmentation => $self->o('tempdir') . '/segmentation', tempdir_regulatory_build => $self->o('tempdir') . '/regulatory_build', data_root_dir => $self->o('data_root_dir'), regulatory_build_name => $self->o('regulatory_build_name'), regulatory_build_description => $self->o('regulatory_build_description'), ensembl_release_version => $self->o('ensembl_release_version'), reference_data_root_dir => $self->o('reference_data_root_dir'), reg_conf => $self->o('reg_conf'), #ChromHMM => '/nfs/production/panda/ensembl/funcgen/ChromHMM/ChromHMM.jar', ChromHMM => '/nfs/production/panda/ensembl/funcgen/ChromHMM/1.17/ChromHMM/ChromHMM.modified.jar', # /nfs/production/panda/ensembl/funcgen/ChromHMM/1.17/ChromHMM # # java -jar /nfs/production/panda/ensembl/funcgen/ChromHMM/1.17/ChromHMM/ChromHMM.modified.jar #export DISPLAY= ; java -Xmx30000m -cp /nfs/production/panda/ensembl/funcgen/ChromHMM/batik-1.10/lib/batik-all-1.10.jar:/nfs/production/panda/ensembl/funcgen/ChromHMM/batik-1.10/lib/batik-all-1.10.jar:/nfs/production/panda/ensembl/funcgen/ChromHMM/htsjdk/build/libs/:/nfs/production/panda/ensembl/funcgen/ChromHMM/jheatchart-0.6/dist/jheatchart-0.52/jheatchart-0.52.jar:/nfs/production/panda/ensembl/funcgen/ChromHMM/ChromHMM/ edu.mit.compbio.ChromHMM.ChromHMM LearnModel -r 300 -p 12 -l #chromosome_length_file# #binarized_bam_dir#/#superclass#/#class#/ #learn_model_directory# 25 #assembly# }; } sub pipeline_analyses { my ($self) = @_; return [ { -logic_name => 'start_segmentation', -module => 'Bio::EnsEMBL::Hive::RunnableDB::Dummy', -flow_into => { MAIN => 'truncate_regulatory_build_tables', }, }, { -logic_name => 'truncate_regulatory_build_tables', -module => 'Bio::EnsEMBL::Hive::RunnableDB::SqlCmd', -parameters => { sql => [ 'truncate regulatory_build;', 'truncate regulatory_feature;', 'truncate regulatory_activity;', 'truncate regulatory_build_epigenome;', 'truncate regulatory_evidence;', 'truncate regulatory_build_statistic;', 'truncate segmentation_file;', 'delete from data_file where table_name = "segmentation_file";', 'truncate segmentation_state_assignment;', 'truncate segmentation_state_emission;', 'truncate segmentation_cell_tables', 'truncate segmentation', ], db_conn => 'funcgen:#species#', }, -flow_into => { MAIN => 'segmentation_job_factory', }, }, { -logic_name => 'segmentation_job_factory', -module => 'Bio::EnsEMBL::Funcgen::RunnableDB::Segmentation::SegmentationJobFactory', -parameters => { tempdir => '#tempdir_segmentation#/#species#/', }, -flow_into => { 2 => 'select_peak_callings_to_use_in_regulatory_build', }, }, { -logic_name => 'select_peak_callings_to_use_in_regulatory_build', -module => 'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd', -parameters => { cmd => q( select_peak_callings_to_use_in_regulatory_build.pl \ --registry #reg_conf# \ --species #species# \ --dry_run 0 ) }, -flow_into => { MAIN => 'create_cell_tables', }, }, { -logic_name => 'create_cell_tables', -module => 'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd', -parameters => { cmd => q( classify_epigenome_to_segmentation_run.pl \ --registry #reg_conf# \ --species #species# \ --partition_by_experimental_group 1 ) }, -flow_into => { MAIN => 'seed_segmentation_jobs', }, }, { -logic_name => 'seed_segmentation_jobs', -module => 'Bio::EnsEMBL::Hive::RunnableDB::JobFactory', -parameters => { db_conn => 'funcgen:#species#', inputquery => ' select distinct superclass, class from segmentation_cell_tables ', }, -flow_into => { '2->A' => { 'record_segmentation_as_done' => INPUT_PLUS({ class => '#class#', superclass => '#superclass#', segmentation_name => '#superclass#_#class#', celltable_file => 'celltable.#superclass#.#class#.txt', learn_model_directory => '#learnmodel_output_dir#/#superclass#/#class#/', }) }, 'A->MAIN' => { 'generate_segmentation_parameter_file' => INPUT_PLUS({ foo => 'bar', }) }, }, }, { -logic_name => 'record_segmentation_as_done', -module => 'Bio::EnsEMBL::Hive::RunnableDB::Dummy', -parameters => { record => { learn_model_directory => '#learn_model_directory#', segmentation_name => '#superclass#_#class#', celltable_file => 'celltable.#superclass#.#class#.txt', } }, -flow_into => { MAIN => [ '?accu_name=segmentation_lists&accu_address={superclass}{class}&accu_input_variable=record', 'make_segmentation_dir' ] }, }, { -logic_name => 'make_segmentation_dir', -module => 'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd', -parameters => { cmd => q( rm -rf #tempdir_segmentation#/#species#/#superclass#/#class# ; ) . q( mkdir -p #tempdir_segmentation#/#species#/#superclass#/#class# ), }, -flow_into => { MAIN => 'generate_cell_table_file', }, }, { -logic_name => 'generate_cell_table_file', -module => 'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd', -parameters => { cmd => q( generate_cell_table_file.pl \ --registry #reg_conf# \ --species #species# \ --superclass #superclass# \ --class #class# \ --cell_table_file #tempdir_segmentation#/#species#/#superclass#/#class#/celltable.#superclass#.#class#.txt ) }, -flow_into => { MAIN => [ 'binarize', ], }, }, { -logic_name => 'binarize', -module => 'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd', -max_retry_count => 0, -rc_name => 'binarization', -parameters => { cmd => q( java -Xmx14500m ) . q( -jar #ChromHMM# ) . q( BinarizeBam ) . q( #chromosome_length_file# ) . q( #data_root_dir_species_assembly# ) . q( #tempdir_segmentation#/#species#/#superclass#/#class#/celltable.#superclass#.#class#.txt ) . q( #binarized_bam_dir#/#superclass#/#class#/ ), }, -flow_into => { MAIN => 'delete_non_chromosomal_files_from_binarization_dir', }, }, { -logic_name => 'delete_non_chromosomal_files_from_binarization_dir', -module => 'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd', -parameters => { cmd => q( delete_non_chromosomal_files_from_binarization_dir.pl \ --registry #reg_conf# \ --species #species# \ --directory #binarized_bam_dir#/#superclass#/#class# ), }, -flow_into => { MAIN => 'learn_model', }, }, { -logic_name => 'learn_model', -module => 'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd', -max_retry_count => 0, -rc_name => 'learn_model', -parameters => { cmd => 'run_ChromHMM_skip_nonsense_errors.pl --cmd "#run_cmd#"', run_cmd => q( export DISPLAY= ; ) . q( java -Xmx30000m ) . q( -jar #ChromHMM# ) . q( LearnModel ) . q( -r 300 -p 12 ) . q( -l #chromosome_length_file# ) . q( #binarized_bam_dir#/#superclass#/#class#/ ) . q( #learn_model_directory# ) . q( 25 ) . q( #assembly# ) }, # -flow_into => { # MAIN => 'record_segmentation_as_done', # }, }, { -logic_name => 'generate_segmentation_parameter_file', -module => 'Bio::EnsEMBL::Funcgen::RunnableDB::Segmentation::GenerateSegmentationParameterFile', -parameters => { file => '#segmentation_parameter_file#', }, -flow_into => { MAIN => { 'make_regbuild_dir' => INPUT_PLUS({ segmentation_lists => '#segmentation_lists#' }) }, }, }, { -logic_name => 'make_regbuild_dir', -module => 'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd', -parameters => { cmd => q(rm -rf #tempdir_regulatory_build#/#species#/#assembly# ; ) . q(mkdir -p #tempdir_regulatory_build#/#species#/#assembly# ), }, -flow_into => { MAIN => 'build_regulatory_features', }, }, { -logic_name => 'build_regulatory_features', -module => 'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd', -rc_name => '32Gb_job', -parameters => { cmd => q( new_build_regulatory_features.pl ) . q( --species #species# ) . q( --out #tempdir_regulatory_build#/#species# ) . q( -dump #segmentation_parameter_file# ) . q( -a #assembly# ) . q( --db #funcgen_dbname# ) . q( --user #funcgen_username# ) . q( --host #funcgen_host# ) . q( --pass #funcgen_password# ) . q( --port #funcgen_port# ) . q( --dnadb_name #core_dbname# ) . q( --dnadb_host #core_host# ) . q( --dnadb_user #core_username# ) . q( --dnadb_pass #core_password# ) . q( --dnadb_port #core_port# ) . q( --chrom_lengths #chromosome_length_file# ) }, -flow_into => { MAIN => [ 'load_build', 'seed_load_assignment_jobs', ] }, }, { -logic_name => 'load_build', -module => 'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd', -rc_name => '64Gb_job', -parameters => { cmd => q( load_build.pl ) . q( --dbname #funcgen_dbname# ) . q( --user #funcgen_username# ) . q( --host #funcgen_host# ) . q( --pass #funcgen_password# ) . q( --port #funcgen_port# ) . q( --dnadb_name #core_dbname# ) . q( --dnadb_host #core_host# ) . q( --dnadb_user #core_username# ) . q( --dnadb_pass #core_password# ) . q( --dnadb_port #core_port# ) . q( --base_dir #tempdir_regulatory_build#/#species#/#assembly# ) }, -flow_into => { MAIN => 'set_regulatory_build_metadata' }, }, { -logic_name => 'set_regulatory_build_metadata', -module => 'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd', -parameters => { cmd => q( set_regulatory_build_metadata.pl \ --species #species# \ --registry #reg_conf# \ --name "#regulatory_build_name#" \ --description "#regulatory_build_description#" \ --release_version #ensembl_release_version# ) }, -flow_into => { MAIN => 'set_sample_regulatory_feature' }, }, { -logic_name => 'set_sample_regulatory_feature', -module => 'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd', -parameters => { cmd => q( set_sample_regulatory_feature.pl \ --species #species# \ --registry #reg_conf# \ ) }, -flow_into => { MAIN => 'populate_meta_coord' }, }, { -logic_name => 'populate_meta_coord', -module => 'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd', -parameters => { cmd => qq( populate_meta_coord.pl ) . qq( --species #species# ) . qq( --registry #reg_conf# ) }, -flow_into => { MAIN => 'populate_regulatory_build_epigenome_table', }, }, { -logic_name => 'seed_load_assignment_jobs', -module => 'Bio::EnsEMBL::Funcgen::RunnableDB::Segmentation::SeedLoadAssignmentJobs', -parameters => { db_conn => 'funcgen:#species#', }, -flow_into => { '2->A' => 'load_state_emissions', 'A->MAIN' => 'load_state_assignments', }, }, { -logic_name => 'load_state_emissions', -module => 'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd', -parameters => { cmd => q( load_state_emissions.pl \ --species #species# \ --registry #reg_conf# \ --emissions_file #learn_model_directory#/emissions_25.txt \ --segmentation #segmentation_name# ) }, }, { -logic_name => 'load_state_assignments', -module => 'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd', -parameters => { cmd => q( load_state_assignments.pl \ --species #species# \ --registry #reg_conf# \ --assignments_file #tempdir_regulatory_build#/#species#/tmp/assignments.txt ) }, }, { -logic_name => 'populate_regulatory_build_epigenome_table', -module => 'Bio::EnsEMBL::Hive::RunnableDB::SqlCmd', -parameters => { sql => [ "truncate regulatory_build_epigenome;", "insert into regulatory_build_epigenome ( regulatory_build_id, epigenome_id ) select distinct regulatory_build_id, epigenome_id from regulatory_build join regulatory_feature using (regulatory_build_id) join regulatory_activity using (regulatory_feature_id); ", ], db_conn => 'funcgen:#species#', }, -flow_into => { MAIN => 'seed_register_segmentation_files_jobs', }, }, { -logic_name => 'seed_register_segmentation_files_jobs', -module => 'Bio::EnsEMBL::Funcgen::RunnableDB::Segmentation::SeedLoadAssignmentJobs', -parameters => { db_conn => 'funcgen:#species#', }, -flow_into => { 2 => 'register_segmentation_files', }, }, { -logic_name => 'register_segmentation_files', -module => 'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd', -parameters => { cmd => q( register_segmentation_files.pl \ --species #species# \ --registry #reg_conf# \ --segmentation_directory #tempdir_regulatory_build#/#species#/#assembly#/segmentations/#segmentation_name# \ --db_file_species_assembly_dir #data_root_dir#/#species#/#assembly#/funcgen/segmentation_file/#ensembl_release_version# \ --db_file_relative_dir /funcgen/segmentation_file/#ensembl_release_version# \ --segmentation_name #segmentation_name# ) }, }, ]; } 1;