From b5e17a6906b1e034ffe8bd18957ee55172002de9 Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Fri, 10 Aug 2012 10:16:41 +0000
Subject: [PATCH] added vega runs in core handover config
---
.../Pipeline/PipeConfig/Core_handover_conf.pm | 27 ++++++++++++++++++-
1 file changed, 26 insertions(+), 1 deletion(-)
diff --git a/modules/Bio/EnsEMBL/Pipeline/PipeConfig/Core_handover_conf.pm b/modules/Bio/EnsEMBL/Pipeline/PipeConfig/Core_handover_conf.pm
index 79a8c74340..987303a8f1 100644
--- a/modules/Bio/EnsEMBL/Pipeline/PipeConfig/Core_handover_conf.pm
+++ b/modules/Bio/EnsEMBL/Pipeline/PipeConfig/Core_handover_conf.pm
@@ -66,7 +66,7 @@ sub pipeline_analyses {
'3->C' => ['CodingDensity'],
'C->3' => ['NonCodingDensity'],
'3->A' => ['PercentRepeat', 'CodingDensity', 'NonCodingDensity', 'PercentGC'],
- '2->A' => ['GeneGC', 'PepStats', 'GeneCount', 'ConstitutiveExons'],
+ '2->A' => ['GeneGC', 'PepStats', 'GeneCount', 'ConstitutiveExons', 'ConstitutiveExonsVega', 'PepStatsVega'],
'A->1' => ['Notify'],
},
},
@@ -94,6 +94,31 @@ sub pipeline_analyses {
-rc_name => 'normal',
},
+ {
+ -logic_name => 'ConstitutiveExonsVega',
+ -module => 'Bio::EnsEMBL::Pipeline::Production::ConstitutiveExons',
+ -parameters => {
+ dbtype => 'vega',
+ },
+ -max_retry_count => 5,
+ -hive_capacity => 10,
+ -rc_name => 'normal',
+ -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,
+ },
+
{
-logic_name => 'GeneCount',
-module => 'Bio::EnsEMBL::Pipeline::Production::GeneCount',
--
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