From 0784b3c4f974fab3f11b9d243c6e7b3dcc2f77fa Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Thu, 26 Jul 2012 15:17:56 +0000
Subject: [PATCH] added gene density related analyses
---
.../Pipeline/PipeConfig/Core_handover_conf.pm | 43 ++++++++++++++++++-
1 file changed, 41 insertions(+), 2 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Pipeline/PipeConfig/Core_handover_conf.pm b/modules/Bio/EnsEMBL/Pipeline/PipeConfig/Core_handover_conf.pm
index 2ff6cc745b..16f15f5490 100644
--- a/modules/Bio/EnsEMBL/Pipeline/PipeConfig/Core_handover_conf.pm
+++ b/modules/Bio/EnsEMBL/Pipeline/PipeConfig/Core_handover_conf.pm
@@ -55,10 +55,49 @@ sub pipeline_analyses {
-flow_into => {
1 => 'Notify',
2 => ['GeneGC', 'PepStats'],
- 3 => ['PercentGC', 'PercentRepeat'],
+ 3 => ['PercentGC', 'PercentRepeat', 'CodingDensity', 'PseudogeneDensity', 'NonCodingDensity'],
},
},
+ {
+ -logic_name => 'CodingDensity',
+ -module => 'Bio::EnsEMBL::Pipeline::Production::CodingDensity',
+ -parameters => {
+ logic_name => 'codingdensity', 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 => 'PseudogeneDensity',
+ -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'),
+ },
+ -max_retry_count => 1,
+ -hive_capacity => 10,
+ -rc_name => 'default',
+ -can_be_empty => 1,
+ },
+
{
-logic_name => 'PercentRepeat',
-module => 'Bio::EnsEMBL::Pipeline::Production::PercentRepeat',
@@ -116,7 +155,7 @@ sub pipeline_analyses {
email => $self->o('email'),
subject => $self->o('pipeline_name').' has finished',
},
- -wait_for => ['PepStats', 'GeneGC', 'PercentGC', 'PercentRepeat'],
+ -wait_for => ['PepStats', 'GeneGC', 'PercentGC', 'PercentRepeat', 'CodingDensity', 'PseudogeneDensity', 'NonCodingDensity'],
}
];
--
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