def start_assembly(args, logger):
'''Start assembly of solid reads'''
import mlst_modules
from mlst_classes import Moab
from mlst_classes import Semaphore
import os
# set queueing
paths = mlst_modules.setSystem()
home = os.getcwd()
if args.partition == 'uv':
cpuV = 'ncpus=%i,mem=%s,walltime=172800' % (args.n, args.m)
cpuA = 'ncpus=1,mem=512mb,walltime=172800'
cpuC = 'ncpus=1,mem=2gb,walltime=172800'
cpuE = 'ncpus=1,mem=5gb,walltime=172800'
cpuF = 'ncpus=2,mem=2gb,walltime=172800'
cpuB = 'ncpus=16,mem=10gb,walltime=172800'
else:
cpuV = 'nodes=1:ppn=%i,mem=%s,walltime=172800' % (args.n, args.m)
cpuA = 'nodes=1:ppn=1,mem=512mb,walltime=172800'
cpuC = 'nodes=1:ppn=1,mem=2gb,walltime=172800'
cpuE = 'nodes=1:ppn=1,mem=5gb,walltime=172800'
cpuF = 'nodes=1:ppn=2,mem=2gb,walltime=172800'
cpuB = 'nodes=1:ppn=16,mem=10gb,walltime=172800'
solid_calls = solid(args)
# set environment variable (add solid binaries to bin):
env_var = 'denovo2=%s' % paths['solid_home']
# submit and release jobs
print "Submitting jobs"
solid_moab = Moab(solid_calls, logfile=logger, runname='run_mlst_solid', queue=args.q, cpu=cpuV, env=env_var, partition=args.partition, host='cge-s2.cbs.dtu.dk')
# release jobs
solid_moab.release(host='cge-s2.cbs.dtu.dk')
def start_assembly(args, logger):
'''start newbler assembly'''
import mlst_modules
from mlst_classes import Moab
from mlst_classes import Semaphore
import os
# set queueing
paths = mlst_modules.setSystem()
home = os.getcwd()
if args.partition == 'uv':
cpuV = 'ncpus=%i,mem=%s,walltime=172800' % (args.n, args.m)
cpuA = 'ncpus=1,mem=512mb,walltime=172800'
cpuC = 'ncpus=1,mem=2gb,walltime=172800'
cpuE = 'ncpus=1,mem=5gb,walltime=172800'
cpuF = 'ncpus=2,mem=2gb,walltime=172800'
cpuB = 'ncpus=16,mem=10gb,walltime=172800'
else:
cpuV = 'nodes=1:ppn=%i,mem=%s,walltime=172800' % (args.n, args.m)
cpuA = 'nodes=1:ppn=1,mem=512mb,walltime=172800'
cpuC = 'nodes=1:ppn=1,mem=2gb,walltime=172800'
cpuE = 'nodes=1:ppn=1,mem=5gb,walltime=172800'
cpuF = 'nodes=1:ppn=2,mem=2gb,walltime=172800'
cpuB = 'nodes=1:ppn=16,mem=10gb,walltime=172800'
newbler_calls = newbler(args)
newblerstats_calls = newbler_stats(args)
# set environment variable (add newbler binaries to bin):
env_var = 'PATH=/panvol1/simon/bin/454/bin/'
# submit and release jobs
print "Submitting jobs"
newbler_moab = Moab(newbler_calls, logfile=logger, runname='run_mlst_newbler', queue=args.q, cpu=cpuV, env=env_var, partition=args.partition, host='cge-s2.cbs.dtu.dk')
newblerstats_moab = Moab(newblerstats_calls, logfile=logger, runname='run_mlst_newblerstats', queue=args.q, cpu=cpuA, depend=True, depend_type='one2one', depend_val=[1], depend_ids=newbler_moab.ids, partition=args.partition, host='cge-s2.cbs.dtu.dk')
# release jobs
newbler_moab.release('cge-s2.cbs.dtu.dk')
newblerstats_moab.release('cge-s2.cbs.dtu.dk')
def start_assembly(args, logger):
'''Start assembly'''
import mlst_modules
from mlst_classes import Moab
from mlst_classes import Semaphore
import os
# set queueing
paths = mlst_modules.setSystem()
home = os.getcwd()
if args.partition == 'uv':
cpuV = 'procs=%i,mem=%s,walltime=172800,flags=sharedmem' % (args.n, args.m)
cpuA = 'procs=1,mem=512mb,walltime=172800,flags=sharedmem'
cpuC = 'procs=1,mem=2gb,walltime=172800,flags=sharedmem'
cpuE = 'procs=1,mem=5gb,walltime=172800,flags=sharedmem'
cpuF = 'procs=2,mem=%s,walltime=172800,flags=sharedmem' % args.m
cpuB = 'procs=16,mem=10gb,walltime=172800,flags=sharedmem'
else:
cpuV = 'nodes=1:ppn=%i,mem=%s,walltime=172800' % (args.n, args.m)
cpuA = 'nodes=1:ppn=1,mem=512mb,walltime=172800'
cpuC = 'nodes=1:ppn=1,mem=2gb,walltime=172800'
cpuE = 'nodes=1:ppn=1,mem=5gb,walltime=172800'
cpuF = 'nodes=1:ppn=2,mem=%s,walltime=172800' % args.m
cpuB = 'nodes=1:ppn=16,mem=10gb,walltime=172800'
# set kmersizes (if auto)
if args.ksizes == ['auto']:
args.ksizes = set_kmersizes(args)
# trimming calls
if args.trim:
illuminatrim_calls = illumina_trim(args, int(args.ksizes[0]), 15, 20, 15, False)
if not os.path.exists('trimmed'):
os.makedirs('trimmed')
# velvet calls
velvet_calls = create_velvet_calls(args)
# velvet parse calls
postprocess_calls = postprocess(args)
# set environment variable:
env_var = 'OMP_NUM_THREADS=%i' % int(args.n - 1)
# submit and release jobs
# NB: mlst_denovo_velvet is run from a compute node, it will then ssh to "host" and submit the jobs from there (cge-s2)
print "Submitting jobs"
# if trimming is needed
if args.trim:
illuminatrim_moab = Moab(illuminatrim_calls, logfile=logger, runname='run_mlst_trim', queue=args.q, cpu=cpuF, partition=args.partition, host='cge-s2.cbs.dtu.dk')
velvet_moab = Moab(velvet_calls, logfile=logger, runname='run_mlst_velvet', queue=args.q, cpu=cpuV, depend=True, depend_type='all', depend_val=[1], depend_ids=illuminatrim_moab.ids, env=env_var, partition=args.partition, host='cge-s2.cbs.dtu.dk')
# if no trimming
else:
velvet_moab = Moab(velvet_calls, logfile=logger, runname='run_mlst_velvet', queue=args.q, cpu=cpuV, env=env_var, partition=args.partition, host='cge-s2.cbs.dtu.dk')
# submit job for postprocessing
postprocess_moab = Moab(postprocess_calls, logfile=logger, runname='run_mlst_postprocess', queue=args.q, cpu=cpuA, depend=True, depend_type='conc', depend_val=[len(velvet_calls)], depend_ids=velvet_moab.ids, partition=args.partition, host='cge-s2.cbs.dtu.dk')
# release jobs
print "Releasing jobs"
if args.trim and len(illuminatrim_calls) > 0: illuminatrim_moab.release(host='cge-s2.cbs.dtu.dk')
velvet_moab.release('cge-s2.cbs.dtu.dk')
postprocess_moab.release(host='cge-s2.cbs.dtu.dk')
