From 4abc4693e0a41a11beed66748a1272627d9fbec8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Tue, 13 Jul 2010 12:49:48 +0000
Subject: [PATCH] Add further parametrization of LSF options. From Dan S.
---
modules/Bio/EnsEMBL/IdMapping/ExonScoreBuilder.pm | 11 ++++++++---
modules/Bio/EnsEMBL/IdMapping/SyntenyFramework.pm | 6 ++++--
2 files changed, 12 insertions(+), 5 deletions(-)
diff --git a/modules/Bio/EnsEMBL/IdMapping/ExonScoreBuilder.pm b/modules/Bio/EnsEMBL/IdMapping/ExonScoreBuilder.pm
index e39cfa7a54..c3908f6a74 100644
--- a/modules/Bio/EnsEMBL/IdMapping/ExonScoreBuilder.pm
+++ b/modules/Bio/EnsEMBL/IdMapping/ExonScoreBuilder.pm
@@ -430,7 +430,10 @@ sub run_exonerate {
$self->logger->debug("$exonerate_job\n\n");
local *BSUB;
- open BSUB, "|bsub -J$lsf_name\[1-$num_jobs\] -o $logpath/exonerate.\%I.out"
+ open BSUB,
+ "|bsub "
+ . $self->conf()->param('lsf_opt_run')
+ . " -J$lsf_name\[1-$num_jobs\] -o $logpath/exonerate.\%I.out"
or $self->logger->error("Could not open open pipe to bsub: $!\n");
print BSUB $exonerate_job;
@@ -441,8 +444,10 @@ sub run_exonerate {
# submit dependent job to monitor finishing of exonerate jobs
$self->logger->info("Waiting for exonerate jobs to finish...\n", 0, 'stamped');
- my $dependent_job = qq{bsub -K -w "ended($lsf_name)" -q small } .
- qq{-o $logpath/exonerate_depend.out /bin/true};
+ my $dependent_job =
+ qq{bsub -K -w "ended($lsf_name)" }
+ . $self->conf()->param('lsf_opt_run_small')
+ . qq{ -o $logpath/exonerate_depend.out /bin/true};
system($dependent_job) == 0 or
$self->logger->error("Error submitting dependent job: $!\n");
diff --git a/modules/Bio/EnsEMBL/IdMapping/SyntenyFramework.pm b/modules/Bio/EnsEMBL/IdMapping/SyntenyFramework.pm
index 0b2c09339f..dff799eea7 100644
--- a/modules/Bio/EnsEMBL/IdMapping/SyntenyFramework.pm
+++ b/modules/Bio/EnsEMBL/IdMapping/SyntenyFramework.pm
@@ -399,8 +399,10 @@ sub rescore_gene_matrix_lsf {
# submit dependent job to monitor finishing of jobs
$self->logger->info("Waiting for jobs to finish...\n", 0, 'stamped');
- my $dependent_job = qq{bsub -K -w "ended($lsf_name)" -q small } .
- qq{-o $logpath/synteny_rescore_depend.out /bin/true};
+ my $dependent_job =
+ qq{bsub -K -w "ended($lsf_name)" }
+ . $self->conf()->param('lsf_opt_run_small')
+ . qq{ -o $logpath/synteny_rescore_depend.out /bin/true};
system($dependent_job) == 0 or
$self->logger->error("Error submitting dependent job: $!\n");
--
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