Commit bc20a3ee authored by Magali Ruffier's avatar Magali Ruffier
Browse files

constitutive exon analysis added to pipeline

slight memory requirement adjustements as well
parent 5e4ef9cf
......@@ -27,7 +27,7 @@ sub default_options {
### Defaults
pipeline_name => 'core_handover_update_'.$self->o('release'),
pipeline_name => 'core_test_'.$self->o('release'),
email => $self->o('ENV', 'USER').'@sanger.ac.uk',
};
......@@ -57,11 +57,33 @@ sub pipeline_analyses {
-input_ids => [ {} ],
-flow_into => {
1 => 'Notify',
2 => ['GeneGC', 'PepStats', 'GeneCount'],
2 => ['GeneGC', 'PepStats', 'GeneCount', 'ConstitutiveExons'],
3 => ['PercentGC', 'PercentRepeat', 'CodingDensity', 'PseudogeneDensity', 'NonCodingDensity'],
},
},
{
-logic_name => 'ConstitutiveExons',
-module => 'Bio::EnsEMBL::Pipeline::Production::ConstitutiveExons',
-max_retry_count => 5,
-hive_capacity => 10,
-rc_name => 'normal',
-can_be_empty => 1,
},
{
-logic_name => 'PepStats',
-module => 'Bio::EnsEMBL::Pipeline::Production::PepStats',
-parameters => {
tmpdir => '/tmp', binpath => '/software/pubseq/bin/emboss',
dbtype => 'core',
},
-max_retry_count => 5,
-hive_capacity => 10,
-rc_name => 'mem',
-can_be_empty => 1,
},
{
-logic_name => 'GeneCount',
-module => 'Bio::EnsEMBL::Pipeline::Production::GeneCount',
......@@ -119,23 +141,10 @@ sub pipeline_analyses {
},
-max_retry_count => 1,
-hive_capacity => 10,
-rc_name => 'normal',
-can_be_empty => 1,
},
{
-logic_name => 'PepStats',
-module => 'Bio::EnsEMBL::Pipeline::Production::PepStats',
-parameters => {
tmpdir => '/tmp', binpath => '/software/pubseq/bin/emboss',
},
-max_retry_count => 5,
-hive_capacity => 10,
-rc_name => 'mem',
-can_be_empty => 1,
},
{
-logic_name => 'GeneGC',
-module => 'Bio::EnsEMBL::Pipeline::Production::GeneGC',
......@@ -154,7 +163,7 @@ sub pipeline_analyses {
},
-max_retry_count => 1,
-hive_capacity => 10,
-rc_name => 'default',
-rc_name => 'normal',
-can_be_empty => 1,
},
......@@ -167,7 +176,7 @@ sub pipeline_analyses {
email => $self->o('email'),
subject => $self->o('pipeline_name').' has finished',
},
-wait_for => ['PepStats', 'GeneGC', 'PercentGC', 'PercentRepeat', 'CodingDensity', 'PseudogeneDensity', 'NonCodingDensity', 'GeneCount'],
-wait_for => ['PepStats', 'GeneGC', 'PercentGC', 'PercentRepeat', 'CodingDensity', 'PseudogeneDensity', 'NonCodingDensity', 'GeneCount', 'ConstitutiveExons'],
}
];
......@@ -192,8 +201,8 @@ sub resource_classes {
my $self = shift;
return {
'default' => { 'LSF' => ''},
'normal' => { 'LSF' => '-q normal -M 400000 -R"select[mem>400] rusage[mem=400]"'},
'mem' => { 'LSF' => '-q normal -M 2500000 -R"select[mem>2500] rusage[mem=2500]"'},
'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]"'},
}
}
......
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