Commit 4abc4693 authored by Andreas Kusalananda Kähäri's avatar Andreas Kusalananda Kähäri
Browse files

Add further parametrization of LSF options. From Dan S.

parent f91f1fc6
...@@ -430,7 +430,10 @@ sub run_exonerate { ...@@ -430,7 +430,10 @@ sub run_exonerate {
$self->logger->debug("$exonerate_job\n\n"); $self->logger->debug("$exonerate_job\n\n");
local *BSUB; 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"); or $self->logger->error("Could not open open pipe to bsub: $!\n");
print BSUB $exonerate_job; print BSUB $exonerate_job;
...@@ -441,8 +444,10 @@ sub run_exonerate { ...@@ -441,8 +444,10 @@ sub run_exonerate {
# submit dependent job to monitor finishing of exonerate jobs # submit dependent job to monitor finishing of exonerate jobs
$self->logger->info("Waiting for exonerate jobs to finish...\n", 0, 'stamped'); $self->logger->info("Waiting for exonerate jobs to finish...\n", 0, 'stamped');
my $dependent_job = qq{bsub -K -w "ended($lsf_name)" -q small } . my $dependent_job =
qq{-o $logpath/exonerate_depend.out /bin/true}; qq{bsub -K -w "ended($lsf_name)" }
. $self->conf()->param('lsf_opt_run_small')
. qq{ -o $logpath/exonerate_depend.out /bin/true};
system($dependent_job) == 0 or system($dependent_job) == 0 or
$self->logger->error("Error submitting dependent job: $!\n"); $self->logger->error("Error submitting dependent job: $!\n");
......
...@@ -399,8 +399,10 @@ sub rescore_gene_matrix_lsf { ...@@ -399,8 +399,10 @@ sub rescore_gene_matrix_lsf {
# submit dependent job to monitor finishing of jobs # submit dependent job to monitor finishing of jobs
$self->logger->info("Waiting for jobs to finish...\n", 0, 'stamped'); $self->logger->info("Waiting for jobs to finish...\n", 0, 'stamped');
my $dependent_job = qq{bsub -K -w "ended($lsf_name)" -q small } . my $dependent_job =
qq{-o $logpath/synteny_rescore_depend.out /bin/true}; qq{bsub -K -w "ended($lsf_name)" }
. $self->conf()->param('lsf_opt_run_small')
. qq{ -o $logpath/synteny_rescore_depend.out /bin/true};
system($dependent_job) == 0 or system($dependent_job) == 0 or
$self->logger->error("Error submitting dependent job: $!\n"); $self->logger->error("Error submitting dependent job: $!\n");
......
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