From 65b0cd8c89511dec3967cff9f485edf005a26689 Mon Sep 17 00:00:00 2001
From: Cedric Cabau <cedric.cabau@inra.fr>
Date: Wed, 19 Apr 2017 15:31:04 +0000
Subject: [PATCH] Get n cpu for bwa.pl from drap.cfg
---
tags/drap-v1.91/runAssessment | 2 +-
trunk/runAssessment | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/tags/drap-v1.91/runAssessment b/tags/drap-v1.91/runAssessment
index a27eaa2..dfe9727 100755
--- a/tags/drap-v1.91/runAssessment
+++ b/tags/drap-v1.91/runAssessment
@@ -532,7 +532,7 @@ sub get_mapping_analysis {
$opt->{binpath}."/bwa.pl --reference %s --R1 %s %s --bam %s -t %s --vmem %s --mem %s%s",
$assembly, join(" ", @{$opt->{R1}}), (scalar(@{$opt->{R2}}) > 0 ? "--R2 ".join(" ", @{$opt->{R2}}) : ""),
$mapping_out_path, $opt->{env}->{n_cpu}, $opt->{memory}, $opt->{memory},$opt->{local_param}
- ), $opt->{local_param} ? 8 : 1
+ ), $opt->{local_param} ? $opt->{env}->{n_cpu} : 1
)
);
diff --git a/trunk/runAssessment b/trunk/runAssessment
index a27eaa2..dfe9727 100755
--- a/trunk/runAssessment
+++ b/trunk/runAssessment
@@ -532,7 +532,7 @@ sub get_mapping_analysis {
$opt->{binpath}."/bwa.pl --reference %s --R1 %s %s --bam %s -t %s --vmem %s --mem %s%s",
$assembly, join(" ", @{$opt->{R1}}), (scalar(@{$opt->{R2}}) > 0 ? "--R2 ".join(" ", @{$opt->{R2}}) : ""),
$mapping_out_path, $opt->{env}->{n_cpu}, $opt->{memory}, $opt->{memory},$opt->{local_param}
- ), $opt->{local_param} ? 8 : 1
+ ), $opt->{local_param} ? $opt->{env}->{n_cpu} : 1
)
);
--
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