beekeeper.pl
The Beekeeper is in charge of interfacing between the Queen and a compute resource or 'compute farm'. Its job is to initialize/sync the eHive database (via the Queen), query the Queen if it needs any workers and to send the requested number of workers to open machines via the runWorker.pl script.
It is also responsible for interfacing with the Queen to identify workers which died unexpectantly so that she can free the dead workers and reclaim unfinished jobs.
beekeeper.pl --host=hostname --port=3306 --user=username --password=secret --database=ehive_dbname -sync
beekeeper.pl -url mysql://username:secret@hostname:port/ehive_dbname -sync
beekeeper.pl -url mysql://username:secret@hostname:port/ehive_dbname
beekeeper.pl -url mysql://username:secret@hostname:port/long_mult_test -local -local_cpus 3 -loop
beekeeper.pl -url mysql://username:secret@hostname:port/long_mult_test -logic_name fast_blast -loop
beekeeper.pl -url mysql://username:secret@hostname:port/long_mult_test -run
beekeeper.pl -url mysql://username:secret@hostname:port/long_mult_test -reset_all_jobs_for_analysis buggy_analysis
beekeeper.pl -url mysql://username:secret@hostname:port/long_mult_test -dead
-conf <path> : config file describing db connection -regfile <path> : path to a Registry configuration file -regname <string> : species/alias name for the Hive DBAdaptor -url <url string> : url defining where hive database is located -host <machine> : mysql database host <machine> -port <port#> : mysql port number -user <name> : mysql connection user <name> -password <pass> : mysql connection password <pass> -database <name> : mysql database <name>
-loop : run autonomously, loops and sleeps -max_loops <num> : perform max this # of loops in autonomous mode -run : run 1 iteration of automation loop -run_job_id <job_id> : run 1 iteration for this job_id -sleep <num> : when looping, sleep <num> minutes (default 2min)
-local : run jobs on local CPU (fork) -local_cpus <num> : max # workers to be running locally -wlimit <num> : max # workers to create per loop -no_pend : don't adjust needed workers by pending workers -lsf_options <string> : passes <string> to LSF bsub command as <options>
-jlimit <num> : #jobs to run before worker can die naturally -batch_size <num> : #jobs a worker can claim at once -lifespan <num> : lifespan limit for each worker -logic_name <string> : restrict the pipeline stat/runs to this analysis logic_name -maximise_concurrency 1 : try to run more different analyses at the same time
-help : print this help -dead : clean dead jobs for resubmission -alldead : all outstanding workers -no_analysis_stats : don't show status of each analysis -worker_stats : show status of each running worker -failed_jobs : show all failed jobs -reset_job_id <num> : reset a job back to READY so it can be rerun -reset_all_jobs_for_analysis <logic_name> : reset jobs back to READY so it can be rerun