=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 . =cut package Bio::EnsEMBL::Variation::Pipeline::ReleaseDataDumps::ReleaseDumps_conf; use strict; use warnings; use Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf; # All Hive databases configuration files should inherit from HiveGeneric, directly or indirectly use base ('Bio::EnsEMBL::Hive::PipeConfig::EnsemblGeneric_conf'); sub default_options { my ($self) = @_; # The hash returned from this function is used to configure the # pipeline, you can supply any of these options on the command # line to override these default values. # You shouldn't need to edit anything in this file other than # these values, if you find you do need to then we should probably # make it an option here, contact the variation team to discuss # this - patches are welcome! return { %{ $self->SUPER::default_options() }, # inherit other stuff from the base class hive_auto_rebalance_semaphores => 1, hive_force_init => 1, hive_use_param_stack => 1, ensembl_release => $self->o('ensembl_release'), # include or exclude the following species from the dumps, run for a division or all the species on the server species => [], antispecies => [], division => [], run_all => 1, pipeline_name => $self->o('pipeline_name'), pipeline_dir => $self->o('pipeline_dir'), registry => $self->o('registry'), script_dir => $self->o('ensembl_cvs_root_dir') . '/ensembl-variation/scripts', gvf_validator => 'gvf_validator', vcf_validator => 'vcf-validator', vcf_sort => 'vcf-sort', so_file => '/nfs/panda/ensembl/production/ensprod/obo_files/SO.obo', tmp_dir => $self->o('tmp_dir'), gvf_readme => $self->o('ensembl_cvs_root_dir') . '/ensembl-variation/modules/Bio/EnsEMBL/Variation/Pipeline/ReleaseDataDumps/README_GVF', gvf_readme_human => $self->o('ensembl_cvs_root_dir') . '/ensembl-variation/modules/Bio/EnsEMBL/Variation/Pipeline/ReleaseDataDumps/README_GVF_human', vcf_readme => $self->o('ensembl_cvs_root_dir') . '/ensembl-variation/modules/Bio/EnsEMBL/Variation/Pipeline/ReleaseDataDumps/README_VCF', vcf_readme_human => $self->o('ensembl_cvs_root_dir') . '/ensembl-variation/modules/Bio/EnsEMBL/Variation/Pipeline/ReleaseDataDumps/README_VCF_human', global_vf_count_in_species => 5_000_000, # if number of vf in a species exceeds this we need to split up dumps max_vf_load => 2_000_000, # group slices together until the vf count exceeds max_vf_load vf_per_slice => 2_000_000, # if number of vf exceeds this we split the slice and dump for each split slice max_split_slice_length => 5e6, # 1e7 debug => 0, # init_pipeline.pl will create the hive database on this machine, naming it # _, and will drop any existing database with this # name pipeline_wide_analysis_capacity => 50, only_finish_dumps => 0, human_population_dumps => 0, pipeline_db => { -host => $self->o('hive_db_host'), -port => $self->o('hive_db_port'), -user => $self->o('hive_db_user'), -pass => $self->o('hive_db_password'), -dbname => $ENV{'USER'} . '_' . $self->o('pipeline_name'), -driver => 'mysql', }, }; } sub pipeline_wide_parameters { my ($self) = @_; return { %{$self->SUPER::pipeline_wide_parameters}, # here we inherit anything from the base class release => $self->o('ensembl_release'), pipeline_dir => $self->o('pipeline_dir'), script_dir => $self->o('script_dir'), so_file => $self->o('so_file'), gvf_validator => $self->o('gvf_validator'), vcf_validator => $self->o('vcf_validator'), vcf_sort => $self->o('vcf_sort'), tmp_dir => $self->o('tmp_dir'), gvf_readme => $self->o('gvf_readme'), vcf_readme => $self->o('vcf_readme'), gvf_readme_human => $self->o('gvf_readme_human'), vcf_readme_human => $self->o('vcf_readme_human'), pipeline_wide_analysis_capacity => $self->o('pipeline_wide_analysis_capacity'), debug => $self->o('debug'), global_vf_count_in_species => $self->o('global_vf_count_in_species'), max_vf_load => $self->o('max_vf_load'), vf_per_slice => $self->o('vf_per_slice'), max_split_slice_length => $self->o('max_split_slice_length'), division => $self->o('division'), registry => $self->o('registry') }; } # Override the default method, to force an automatic loading of the registry in all workers sub beekeeper_extra_cmdline_options { my ($self) = @_; return ' -reg_conf ' . $self->o('registry'), ; } sub resource_classes { my ($self) = @_; return { %{$self->SUPER::resource_classes}, 'default' => { 'LSF' => '-q production-rh7 -R"select[mem>3500] rusage[mem=3500]" -M3500'}, 'urgent' => { 'LSF' => '-q production-rh7 -R"select[mem>2000] rusage[mem=2000]" -M2000'}, 'highmem' => { 'LSF' => '-q production-rh7 -R"select[mem>15000] rusage[mem=15000]" -M15000'}, # this is Sanger LSF speak for "give me 15GB of memory" 'long' => { 'LSF' => '-q production-rh7 -R"select[mem>2000] rusage[mem=2000]" -M2000'}, }; } sub pipeline_analyses { my ($self) = @_; my @analyses; push @analyses, ( { -logic_name => 'species_factory', -module => 'Bio::EnsEMBL::Production::Pipeline::Common::SpeciesFactory', -parameters => { species => $self->o('species'), antispecies => $self->o('antispecies'), division => $self->o('division'), run_all => $self->o('run_all'), }, -input_ids => [{}], -rc_name => 'default', -hive_capacity => 1, -max_retry_count => 0, -flow_into => { 4 => WHEN( '#only_finish_dumps#' => 'finish_dumps', ELSE 'pre_run_checks_gvf_dumps', ) }, }, { -logic_name => 'pre_run_checks_gvf_dumps', -module => 'Bio::EnsEMBL::Variation::Pipeline::ReleaseDataDumps::PreRunChecks', -max_retry_count => 0, -flow_into => { 1 => ['generate_config'], }, -parameters => { 'file_type' => 'gvf', }, }, { -logic_name => 'generate_config', -module => 'Bio::EnsEMBL::Variation::Pipeline::ReleaseDataDumps::Config', -max_retry_count => 0, -rc_name => 'default', -flow_into => { '2->A' => ['init_dump'], 'A->1' => ['join_split_slice'], } }, { -logic_name => 'init_dump', -module => 'Bio::EnsEMBL::Variation::Pipeline::ReleaseDataDumps::InitSubmitJob', -max_retry_count => 0, -analysis_capacity => $self->o('pipeline_wide_analysis_capacity'), -flow_into => { 2 => ['submit_job_gvf_dumps'], }, -parameters => { 'file_type' => 'gvf', 'job_type' => 'dump', }, -rc_name => 'default', }, { -logic_name => 'submit_job_gvf_dumps', -module => 'Bio::EnsEMBL::Variation::Pipeline::ReleaseDataDumps::SubmitJob', -analysis_capacity => $self->o('pipeline_wide_analysis_capacity'), -max_retry_count => 0, -rc_name => 'default', }, # join split slice { -logic_name => 'join_split_slice', -module => 'Bio::EnsEMBL::Variation::Pipeline::ReleaseDataDumps::JoinDump', -analysis_capacity => $self->o('pipeline_wide_analysis_capacity'), -parameters => { 'mode' => 'join_slice_split', 'file_type' => 'gvf', }, -flow_into => { '2->A' => ['init_validate_gvf'], 'A->1' => ['summary_validate_gvf'], }, }, # validate { -logic_name => 'init_validate_gvf', -module => 'Bio::EnsEMBL::Variation::Pipeline::ReleaseDataDumps::InitValidation', -analysis_capacity => $self->o('pipeline_wide_analysis_capacity'), -flow_into => { 2 => ['validate_gvf'], }, -parameters => { 'file_type' => 'gvf', }, }, { -logic_name => 'validate_gvf', -module => 'Bio::EnsEMBL::Variation::Pipeline::ReleaseDataDumps::Validate', -parameters => { 'file_type' => 'gvf', 'so_file' => $self->o('so_file'), 'gvf_validator' => $self->o('gvf_validator'), }, }, { -logic_name => 'summary_validate_gvf', # die if Error? -module => 'Bio::EnsEMBL::Variation::Pipeline::ReleaseDataDumps::SummariseValidation', -parameters => { 'file_type' => 'gvf', }, -flow_into => { 1 => ['cleanup_gvf_dumps'], }, }, # cleanup gvf dumps { -logic_name => 'cleanup_gvf_dumps', -analysis_capacity => $self->o('pipeline_wide_analysis_capacity'), -module => 'Bio::EnsEMBL::Variation::Pipeline::ReleaseDataDumps::FileUtils', -parameters => { 'mode' => 'post_gvf_dump_cleanup', }, -flow_into => { 1 => ['pre_run_checks_gvf2vcf'], }, }, # gvf2vcf { -logic_name => 'pre_run_checks_gvf2vcf', -module => 'Bio::EnsEMBL::Variation::Pipeline::ReleaseDataDumps::PreRunChecks', -max_retry_count => 0, -flow_into => { '2->A' => ['init_parse'], 'A->1' => ['summary_validate_vcf'] }, -parameters => { 'file_type' => 'vcf', }, }, { -logic_name => 'init_parse', -module => 'Bio::EnsEMBL::Variation::Pipeline::ReleaseDataDumps::InitSubmitJob', -flow_into => { 2 => ['submit_job_gvf2vcf'], }, -parameters => { 'file_type' => 'vcf', 'job_type' => 'parse', }, }, { -logic_name => 'submit_job_gvf2vcf', -module => 'Bio::EnsEMBL::Variation::Pipeline::ReleaseDataDumps::SubmitJob', -analysis_capacity => $self->o('pipeline_wide_analysis_capacity'), -flow_into => { 2 => ['validate_vcf'], }, }, { -logic_name => 'validate_vcf', -module => 'Bio::EnsEMBL::Variation::Pipeline::ReleaseDataDumps::Validate', -parameters => { 'file_type' => 'vcf', }, }, { -logic_name => 'summary_validate_vcf', -module => 'Bio::EnsEMBL::Variation::Pipeline::ReleaseDataDumps::SummariseValidation', -parameters => { 'file_type' => 'vcf', }, -flow_into => { 1 => ['cleanup_gvf2vcf'], }, }, { -logic_name => 'cleanup_gvf2vcf', -module => 'Bio::EnsEMBL::Variation::Pipeline::ReleaseDataDumps::FileUtils', -parameters => { 'mode' => 'post_gvf2vcf_cleanup', }, -flow_into => { '2->A' => ['init_join_dumps'], 'A->1' => ['cleanup_dumps'] }, }, { -logic_name => 'init_join_dumps', -module => 'Bio::EnsEMBL::Variation::Pipeline::ReleaseDataDumps::InitJoinDump', -flow_into => { 2 => ['join_dumps'], }, }, { -logic_name => 'join_dumps', -module => 'Bio::EnsEMBL::Variation::Pipeline::ReleaseDataDumps::JoinDump', }, { -logic_name => 'cleanup_dumps', -module => 'Bio::EnsEMBL::Variation::Pipeline::ReleaseDataDumps::CleanUp', -parameters => { 'mode' => 'post_join_dumps', }, -flow_into => { 1 => ['finish_dumps'], }, }, { -logic_name => 'finish_dumps', -module => 'Bio::EnsEMBL::Variation::Pipeline::ReleaseDataDumps::Finish', -parameters => { 'gvf_readme' => $self->o('gvf_readme'), 'vcf_readme' => $self->o('vcf_readme'), 'gvf_readme_human' => $self->o('gvf_readme_human'), 'vcf_readme_human' => $self->o('vcf_readme_human'), } }, ); return \@analyses; } 1;