Commit b8a7c680 authored by Magali Ruffier's avatar Magali Ruffier
Browse files

added config file for analyses to run after otherfeatures handover

parent 7e845316
package Bio::EnsEMBL::Pipeline::PipeConfig::Otherf_handover_conf;
use strict;
use warnings;
use base ('Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf');
use Bio::EnsEMBL::ApiVersion qw/software_version/;
sub default_options {
my ($self) = @_;
return {
# inherit other stuff from the base class
%{ $self->SUPER::default_options() },
### OVERRIDE
### Optional overrides
species => [],
release => software_version(),
run_all => 0,
### Defaults
pipeline_name => 'otherf_handover_update_'.$self->o('release'),
email => $self->o('ENV', 'USER').'@sanger.ac.uk',
};
}
sub pipeline_create_commands {
my ($self) = @_;
return [
# inheriting database and hive tables' creation
@{$self->SUPER::pipeline_create_commands},
];
}
## See diagram for pipeline structure
sub pipeline_analyses {
my ($self) = @_;
return [
{
-logic_name => 'ScheduleSpecies',
-module => 'Bio::EnsEMBL::Pipeline::Production::ClassSpeciesFactory',
-parameters => {
species => $self->o('species'),
run_all => $self->o('run_all')
},
-input_ids => [ {} ],
-flow_into => {
1 => 'Notify',
2 => ['PepStatsOtherf', 'PepStatsVega'],
},
},
{
-logic_name => 'PepStatsOtherf',
-module => 'Bio::EnsEMBL::Pipeline::Production::PepStats',
-parameters => {
tmpdir => '/tmp', binpath => '/software/pubseq/bin/emboss',
dbtype => 'otherfeatures',
},
-max_retry_count => 5,
-hive_capacity => 10,
-rc_name => 'mem',
-can_be_empty => 1,
},
{
-logic_name => 'PepStatsVega',
-module => 'Bio::EnsEMBL::Pipeline::Production::PepStats',
-parameters => {
tmpdir => '/tmp', binpath => '/software/pubseq/bin/emboss',
dbtype => 'vega',
},
-max_retry_count => 5,
-hive_capacity => 10,
-rc_name => 'mem',
-can_be_empty => 1,
},
####### NOTIFICATION
{
-logic_name => 'Notify',
-module => 'Bio::EnsEMBL::Pipeline::Production::EmailSummaryCore',
-parameters => {
email => $self->o('email'),
subject => $self->o('pipeline_name').' has finished',
},
-wait_for => ['PepStatsOtherf', 'PepStatsVega'],
}
];
}
sub pipeline_wide_parameters {
my ($self) = @_;
return {
%{ $self->SUPER::pipeline_wide_parameters() }, # inherit other stuff from the base class
release => $self->o('release'),
};
}
# override the default method, to force an automatic loading of the registry in all workers
sub beekeeper_extra_cmdline_options {
my $self = shift;
return "-reg_conf ".$self->o("registry");
}
sub resource_classes {
my $self = shift;
return {
'default' => { 'LSF' => ''},
'normal' => { 'LSF' => '-q normal -M 500000 -R"select[mem>500] rusage[mem=500]"'},
'mem' => { 'LSF' => '-q normal -M 1000000 -R"select[mem>1000] rusage[mem=1000]"'},
}
}
1;
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