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 {
$self->logger->debug("$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");
......
......@@ -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");
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment