From 3f1f00ae55b6a2ae6a36031c307c7be354aea60b Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Wed, 8 Aug 2012 09:08:50 +0000
Subject: [PATCH] added max_run option, default set to 100
hive and memory requirement adjusted
added some dependencies between analyses to prevent interferences
---
.../Pipeline/PipeConfig/Core_handover_conf.pm | 94 ++++++++++---------
1 file changed, 49 insertions(+), 45 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Pipeline/PipeConfig/Core_handover_conf.pm b/modules/Bio/EnsEMBL/Pipeline/PipeConfig/Core_handover_conf.pm
index 039c3c0e2c..3bcb56580e 100644
--- a/modules/Bio/EnsEMBL/Pipeline/PipeConfig/Core_handover_conf.pm
+++ b/modules/Bio/EnsEMBL/Pipeline/PipeConfig/Core_handover_conf.pm
@@ -24,10 +24,12 @@ sub default_options {
run_all => 0,
bin_count => '150',
+
+ max_run => '100',
### Defaults
- pipeline_name => 'core_test_'.$self->o('release'),
+ pipeline_name => 'core_handover_update_'.$self->o('release'),
email => $self->o('ENV', 'USER').'@sanger.ac.uk',
};
@@ -52,13 +54,15 @@ sub pipeline_analyses {
-module => 'Bio::EnsEMBL::Pipeline::Production::ClassSpeciesFactory',
-parameters => {
species => $self->o('species'),
- run_all => $self->o('run_all')
+ run_all => $self->o('run_all'),
+ max_run => $self->o('max_run')
+
},
-input_ids => [ {} ],
-flow_into => {
1 => 'Notify',
2 => ['GeneGC', 'PepStats', 'GeneCount', 'ConstitutiveExons'],
- 3 => ['PercentGC', 'PercentRepeat', 'CodingDensity', 'PseudogeneDensity', 'NonCodingDensity'],
+ 3 => ['PercentGC', 'PercentRepeat', 'CodingDensity', 'NonCodingDensity', 'PseudogeneDensity'],
},
},
@@ -69,9 +73,8 @@ sub pipeline_analyses {
dbtype => 'core',
},
-max_retry_count => 5,
- -hive_capacity => 10,
+ -hive_capacity => 100,
-rc_name => 'normal',
- -can_be_empty => 1,
},
{
@@ -82,31 +85,30 @@ sub pipeline_analyses {
dbtype => 'core',
},
-max_retry_count => 5,
- -hive_capacity => 10,
+ -hive_capacity => 100,
-rc_name => 'mem',
- -can_be_empty => 1,
},
{
-logic_name => 'GeneCount',
-module => 'Bio::EnsEMBL::Pipeline::Production::GeneCount',
-max_retry_count => 1,
- -hive_capacity => 10,
- -rc_name => 'default',
- -can_be_empty => 1,
+ -hive_capacity => 100,
+ -rc_name => 'normal',
},
{
- -logic_name => 'CodingDensity',
- -module => 'Bio::EnsEMBL::Pipeline::Production::CodingDensity',
+ -logic_name => 'NonCodingDensity',
+ -module => 'Bio::EnsEMBL::Pipeline::Production::NonCodingDensity',
-parameters => {
- logic_name => 'codingdensity', value_type => 'sum',
- bin_count => $self->o('bin_count'),
+ logic_name => 'noncodingdensity', value_type => 'sum',
+ bin_count => $self->o('bin_count'), max_run => $self->o('max_run'),
},
-max_retry_count => 1,
- -hive_capacity => 10,
- -rc_name => 'default',
+ -hive_capacity => 100,
+ -rc_name => 'normal',
-can_be_empty => 1,
+ -wait_for => ['GeneGC', 'CodingDensity'],
},
{
@@ -114,37 +116,25 @@ sub pipeline_analyses {
-module => 'Bio::EnsEMBL::Pipeline::Production::PseudogeneDensity',
-parameters => {
logic_name => 'pseudogenedensity', value_type => 'sum',
- bin_count => $self->o('bin_count'),
- },
- -max_retry_count => 1,
- -hive_capacity => 10,
- -rc_name => 'default',
- -can_be_empty => 1,
- },
-
- {
- -logic_name => 'NonCodingDensity',
- -module => 'Bio::EnsEMBL::Pipeline::Production::NonCodingDensity',
- -parameters => {
- logic_name => 'noncodingdensity', value_type => 'sum',
- bin_count => $self->o('bin_count'),
+ bin_count => $self->o('bin_count'), max_run => $self->o('max_run'),
},
-max_retry_count => 1,
- -hive_capacity => 10,
- -rc_name => 'default',
+ -hive_capacity => 100,
+ -rc_name => 'normal',
-can_be_empty => 1,
+ -wait_for => ['ConstitutiveExons', 'NonCodingDensity', 'CodingDensity'],
},
{
- -logic_name => 'PercentRepeat',
- -module => 'Bio::EnsEMBL::Pipeline::Production::PercentRepeat',
+ -logic_name => 'CodingDensity',
+ -module => 'Bio::EnsEMBL::Pipeline::Production::CodingDensity',
-parameters => {
- logic_name => 'percentagerepeat', value_type => 'ratio',
- bin_count => $self->o('bin_count'),
+ logic_name => 'codingdensity', value_type => 'sum',
+ bin_count => $self->o('bin_count'), max_run => $self->o('max_run'),
},
-max_retry_count => 1,
- -hive_capacity => 10,
- -rc_name => 'mem',
+ -hive_capacity => 100,
+ -rc_name => 'normal',
-can_be_empty => 1,
},
@@ -152,9 +142,8 @@ sub pipeline_analyses {
-logic_name => 'GeneGC',
-module => 'Bio::EnsEMBL::Pipeline::Production::GeneGC',
-max_retry_count => 1,
- -hive_capacity => 10,
+ -hive_capacity => 100,
-rc_name => 'normal',
- -can_be_empty => 1,
},
{
@@ -162,12 +151,27 @@ sub pipeline_analyses {
-module => 'Bio::EnsEMBL::Pipeline::Production::PercentGC',
-parameters => {
table => 'repeat', logic_name => 'percentgc', value_type => 'ratio',
- bin_count => $self->o('bin_count'),
+ bin_count => $self->o('bin_count'), max_run => $self->o('max_run'),
},
-max_retry_count => 1,
- -hive_capacity => 10,
+ -hive_capacity => 100,
-rc_name => 'normal',
-can_be_empty => 1,
+ -wait_for => ['PercentRepeat'],
+ },
+
+ {
+ -logic_name => 'PercentRepeat',
+ -module => 'Bio::EnsEMBL::Pipeline::Production::PercentRepeat',
+ -parameters => {
+ logic_name => 'percentagerepeat', value_type => 'ratio',
+ bin_count => $self->o('bin_count'), max_run => $self->o('max_run'),
+ },
+ -max_retry_count => 1,
+ -hive_capacity => 100,
+ -rc_name => 'mem',
+ -can_be_empty => 1,
+ -wait_for => ['CodingDensity', 'NonCodingDensity', 'PseudogeneDensity'],
},
####### NOTIFICATION
@@ -203,9 +207,9 @@ sub beekeeper_extra_cmdline_options {
sub resource_classes {
my $self = shift;
return {
- 'default' => { 'LSF' => '-R"select[myens_stag1tok>800 && myens_stag2tok>800] rusage[myens_stag1tok=10:myens_stag2tok=10:duration=10]"'},
- 'normal' => { 'LSF' => '-q normal -M 500000 -R"select[mem>500 && myens_stag1tok>800 && myens_stag2tok>800] rusage[mem=500:myens_stag1tok=10:myens_stag2tok=10:duration=10]"'},
- 'mem' => { 'LSF' => '-q normal -M 1000000 -R"select[mem>1000 && myens_stag1tok>800 && myens_stag2tok>800] rusage[mem=1000:myens_stag1tok=10:myens_stag2tok=10:duration=10]"'},
+ 'default' => { 'LSF' => '-q normal -M 500000 -R"select[mem>500 && myens_stag1tok>800 && myens_stag2tok>800] rusage[mem=500:myens_stag1tok=10:myens_stag2tok=10:duration=10]"'},
+ 'normal' => { 'LSF' => '-q normal -M 1000000 -R"select[mem>1000 && myens_stag1tok>800 && myens_stag2tok>800] rusage[mem=1000:myens_stag1tok=10:myens_stag2tok=10:duration=10]"'},
+ 'mem' => { 'LSF' => '-q normal -M 1500000 -R"select[mem>1500 && myens_stag1tok>800 && myens_stag2tok>800] rusage[mem=1500:myens_stag1tok=10:myens_stag2tok=10:duration=10]"'},
}
}
--
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