diff --git a/scripts/beekeeper.pl b/scripts/beekeeper.pl index 0800c4f417402663e77876ce78d75fce494b9ede..3584f63186582081e8c117152b1f7f6060b7f025 100755 --- a/scripts/beekeeper.pl +++ b/scripts/beekeeper.pl @@ -73,7 +73,7 @@ GetOptions('help' => \$help, 'failed_jobs' => \$self->{'show_failed_jobs'}, 'reset_job_id=i' => \$self->{'reset_job_id'}, 'reset_all|reset_all_jobs_for_analysis=s' => \$self->{'reset_all_jobs_for_analysis'}, - 'remove|remove_analysis_id=s' => \$self->{'remove_analysis_id'}, + 'delete|remove=s' => \$self->{'remove_analysis_id'}, # careful 'lsf_options=s' => \$self->{'lsf_options'}, 'job_output=i' => \$self->{'show_job_output'}, 'regfile=s' => \$regfile, @@ -215,7 +215,6 @@ sub usage { print " -no_analysis_stats : don't show status of each analysis\n"; print " -worker_stats : show status of each running worker\n"; print " -failed_jobs : show all failed jobs\n"; - #print " -job_output <job_id> : print stdout/stderr from job_id\n"; print " -reset_job_id <num> : reset a job back to READY so it can be rerun\n"; print " -reset_all_jobs_for_analysis <logic_name>\n"; print " : reset jobs back to READY so it can be rerun\n"; @@ -362,6 +361,7 @@ sub show_running_workers { $worker->process_id, $worker->host, $worker->last_check_in); + printf("%s\n", $worker->output_dir) if ($self->{'verbose_stats'}); } } @@ -577,8 +577,11 @@ sub reset_all_jobs_for_analysis { sub remove_analysis_id { my $self = shift; + require Bio::EnsEMBL::DBSQL::AnalysisAdaptor or die "$!"; + my $analysis = $self->{'dba'}->get_AnalysisAdaptor-> fetch_by_dbID($self->{'remove_analysis_id'}); $self->{'dba'}->get_AnalysisJobAdaptor->remove_analysis_id($analysis->dbID); + $self->{'dba'}->get_AnalysisAdaptor->remove($analysis); }