def lfs_setstripe_maybe(path='.', stripe=12):
path = os.path.abspath(path)
cmd = 'lfs setstripe -c {:d} {!s}'.format(stripe, path)
try:
capture(cmd)
log.info(
'Lustre filesystem detected. This lfs stripe ({}) should propagate to subdirs of {!r}.'
.format(stripe, path))
except Exception as exc:
log.info('Apparently {!r} is not in lustre filesystem, which is fine.'.
format(path))
def submit(self, state, exe, script_fn):
"""Run in cwd, in background.
Can raise.
"""
run_dir = os.getcwd()
job_name = self.get_job_name()
#job_nproc = self.job_nproc
#job_mb = self.job_mb
#job_queue = self.job_queue
# Add shebang, in case shell_start_mode=unix_behavior (for SGE).
# https://github.com/PacificBiosciences/FALCON/pull/348
with open(script_fn, 'r') as original: data = original.read()
with open(script_fn, 'w') as modified: modified.write("#!/bin/bash" + "\n" + data)
mapping = dict(
JOB_EXE='/bin/bash',
JOB_NAME=job_name,
#JOB_OPTS=JOB_OPTS,
#JOB_QUEUE=job_queue,
JOB_SCRIPT=script_fn, CMD=script_fn,
JOB_DIR=run_dir, DIR=run_dir,
JOB_STDOUT='stdout', STDOUT_FILE='stdout',
JOB_STDERR='stderr', STDERR_FILE='stderr',
#MB=pypeflow_mb,
#NPROC=pypeflow_nproc,
)
mapping.update(self.job_dict)
if 'JOB_OPTS' in mapping:
# a special two-level mapping: ${JOB_OPTS} is substituted first
mapping['JOB_OPTS'] = self.sub(mapping['JOB_OPTS'], mapping)
sge_cmd = self.sub(self.submit_template, mapping)
self.submit_capture = capture(sge_cmd)
def submit(self, state, exe, script_fn):
"""Run in cwd, in background.
Can raise.
"""
run_dir = os.getcwd()
job_name = self.get_job_name()
#job_nproc = self.job_nproc
#job_mb = self.job_mb
#job_queue = self.job_queue
# Add shebang, in case shell_start_mode=unix_behavior (for SGE).
# https://github.com/PacificBiosciences/FALCON/pull/348
with open(script_fn, 'r') as original: data = original.read()
with open(script_fn, 'w') as modified: modified.write("#!/bin/bash" + "\n" + data)
mapping = dict(
JOB_EXE='/bin/bash',
JOB_NAME=job_name,
#JOB_OPTS=JOB_OPTS,
#JOB_QUEUE=job_queue,
JOB_SCRIPT=script_fn, CMD=script_fn,
JOB_DIR=run_dir, DIR=run_dir,
JOB_STDOUT='stdout', STDOUT_FILE='stdout',
JOB_STDERR='stderr', STDERR_FILE='stderr',
#MB=pypeflow_mb,
#NPROC=pypeflow_nproc,
)
mapping.update(self.job_dict)
if 'JOB_OPTS' in mapping:
# a special two-level mapping: ${JOB_OPTS} is substituted first
mapping['JOB_OPTS'] = self.sub(mapping['JOB_OPTS'], mapping)
sge_cmd = self.sub(self.submit_template, mapping)
self.submit_capture = capture(sge_cmd)
def validate_config(config):
# This simple and quick check catches common problems early.
# This code might go somewhere else someday.
smrt_bin_cmds = [
'blasr', 'samtools', 'pbalign', 'variantCaller',
]
path_cmds = [
'nucmer',
'show-coords',
'fc_rr_hctg_track2.exe',
]
LOG.info('PATH={}'.format(os.environ['PATH']))
try:
capture('which which')
except Exception:
LOG.warning('Could not find "which" command. Skipping checks for "blasr", etc.')
return
for cmd in smrt_bin_cmds + path_cmds:
syscall('which ' + cmd)
syscall('show-coords -h')
syscall('nucmer --version')