=head1 LICENSE Copyright (c) 1999-2013 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/legal/code_licence.html =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::VariationConsequence_conf; use strict; use warnings; use base ('Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_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 { # general pipeline options that you should change to suit your environment # the location of your checkout of the ensembl API (the hive looks for SQL files here) ensembl_cvs_root_dir => $ENV{'HOME'}.'/ensembl-branches/HEAD', # a name for your pipeline (will also be used in the name of the hive database) pipeline_name => 'variation_consequence', # a directory to keep hive output files and your registry file, you should # create this if it doesn't exist pipeline_dir => '/lustre/scratch103/ensembl/gr5/'.$self->o('pipeline_name'), # a directory where hive workers will dump STDOUT and STDERR for their jobs # if you use lots of workers this directory can get quite big, so it's # a good idea to keep it on lustre, or some other place where you have a # healthy quota! output_dir => $self->o('pipeline_dir').'/hive_output', # a standard ensembl registry file containing connection parameters # for your target database(s) (and also possibly aliases for your species # of interest that you can then supply to init_pipeline.pl with the -species # option) reg_file => $self->o('pipeline_dir').'/ensembl.registry', # if set to 1 this option tells the transcript_effect analysis to disambiguate # ambiguity codes in single nucleotide alleles, so e.g. an allele string like # 'T/M' will be treated as if it were 'T/A/C' (this was a request from ensembl # genomes and we don't use it by default in the ensembl variation pipeline) disambiguate_single_nucleotide_alleles => 0, # configuration for the various resource options used in the pipeline # EBI farm users should either change these here, or override them on the # command line to suit the EBI farm. The names of each option hopefully # reflect their usage, but you may want to change the details (memory # requirements, queue parameters etc.) to suit your own data default_lsf_options => '-R"select[mem>2000] rusage[mem=2000]" -M2000000', urgent_lsf_options => '-q yesterday -R"select[mem>2000] rusage[mem=2000]" -M2000000', highmem_lsf_options => '-R"select[mem>15000] rusage[mem=15000]" -M15000000', # this is Sanger LSF speak for "give me 15GB of memory" long_lsf_options => '-q long -R"select[mem>2000] rusage[mem=2000]" -M2000000', # options controlling the number of workers used for the parallelisable analyses # these default values seem to work for most species transcript_effect_capacity => 50, set_variation_class_capacity => 10, # set this flag to 1 to include LRG transcripts in the transcript effect analysis include_lrg => 1, # these flags control which parts of the pipeline are run run_transcript_effect => 1, run_variation_class => 1, # connection parameters for the hive database, you should supply the hive_db_password # option on the command line to init_pipeline.pl (parameters for the target database # should be set in the registry file defined above) # Should hive use triggeres? hive_use_triggers => 0, # init_pipeline.pl will create the hive database on this machine, naming it # _, and will drop any existing database with this # name hive_db_host => 'ens-variation', hive_db_port => 3306, hive_db_user => 'ensadmin', 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').'_'.$self->o('species'), }, }; } sub pipeline_create_commands { my ($self) = @_; return [ 'mysql '.$self->dbconn_2_mysql('pipeline_db', 0).q{-e 'DROP DATABASE IF EXISTS }.$self->o('pipeline_db', '-dbname').q{'}, @{$self->SUPER::pipeline_create_commands}, 'mysql '.$self->dbconn_2_mysql('pipeline_db', 1).q{-e 'INSERT INTO meta (meta_key, meta_value) VALUES ("hive_output_dir", "}.$self->o('output_dir').q{")'}, ]; } sub resource_classes { my ($self) = @_; return { 'default' => { 'LSF' => $self->o('default_lsf_options') }, 'urgent' => { 'LSF' => $self->o('urgent_lsf_options') }, 'highmem' => { 'LSF' => $self->o('highmem_lsf_options') }, 'long' => { 'LSF' => $self->o('long_lsf_options') }, }; } sub pipeline_analyses { my ($self) = @_; my @common_params = ( ensembl_registry => $self->o('reg_file'), species => $self->o('species'), ); my @analyses; if ($self->o('run_transcript_effect')) { push @analyses, ( { -logic_name => 'init_transcript_effect', -module => 'Bio::EnsEMBL::Variation::Pipeline::InitTranscriptEffect', -parameters => { include_lrg => $self->o('include_lrg'), @common_params, }, -input_ids => [{}], -rc_name => 'default', -flow_into => { 2 => [ 'rebuild_tv_indexes' ], 3 => [ 'update_variation_feature' ], 4 => [ 'transcript_effect' ], 5 => [ 'check_transcript_variation' ], }, }, { -logic_name => 'transcript_effect', -module => 'Bio::EnsEMBL::Variation::Pipeline::TranscriptEffect', -parameters => { disambiguate_single_nucleotide_alleles => $self->o('disambiguate_single_nucleotide_alleles'), @common_params, }, -input_ids => [], -hive_capacity => $self->o('transcript_effect_capacity'), -rc_name => 'default', -flow_into => {}, }, { -logic_name => 'rebuild_tv_indexes', -module => 'Bio::EnsEMBL::Variation::Pipeline::RebuildIndexes', -parameters => { @common_params, }, -input_ids => [], -hive_capacity => 1, -rc_name => 'urgent', -wait_for => [ 'transcript_effect' ], -flow_into => {}, }, { -logic_name => 'check_transcript_variation', -module => 'Bio::EnsEMBL::Variation::Pipeline::CheckTranscriptVariation', -parameters => { pipeline_dir => $self->o('pipeline_dir'), @common_params, }, -input_ids => [], -hive_capacity => 1, -rc_name => 'default', -wait_for => [ 'rebuild_tv_indexes' ], -flow_into => {}, }, { -logic_name => 'update_variation_feature', -module => 'Bio::EnsEMBL::Variation::Pipeline::UpdateVariationFeature', -parameters => { @common_params, }, -input_ids => [], -hive_capacity => 1, -rc_name => 'urgent', -wait_for => [ 'rebuild_tv_indexes' ], -flow_into => {}, }, ); } if ($self->o('run_variation_class')) { push @analyses, ( { -logic_name => 'init_variation_class', -module => 'Bio::EnsEMBL::Variation::Pipeline::InitVariationClass', -parameters => { num_chunks => 50, @common_params, }, -input_ids => [{}], -hive_capacity => 1, -rc_name => 'highmem', -wait_for => ( $self->o('run_transcript_effect') ? [ 'update_variation_feature' ] : [] ), -flow_into => { 1 => [ 'finish_variation_class' ], 2 => [ 'set_variation_class' ], }, }, { -logic_name => 'set_variation_class', -module => 'Bio::EnsEMBL::Variation::Pipeline::SetVariationClass', -parameters => { @common_params, }, -input_ids => [], -hive_capacity => $self->o('set_variation_class_capacity'), -rc_name => 'default', -flow_into => {}, }, { -logic_name => 'finish_variation_class', -module => 'Bio::EnsEMBL::Variation::Pipeline::FinishVariationClass', -parameters => { @common_params, }, -input_ids => [], -hive_capacity => 1, -rc_name => 'urgent', -wait_for => [ 'set_variation_class' ], -flow_into => {}, }, ); } return \@analyses; } 1;