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self.cores = params['cores']
self.output_parent = params['output_parent']
self.testmode = params['testmode']
# Set up logger
logger_kwargs = logger_kwargs or {}
default_logname = ".".join([__name__, self.__class__.__name__, self.name])
if not args:
# strict is only for logger_via_cli.
kwds = {k: v for k, v in logger_kwargs.items() if k != "strict"}
try:
name = kwds.pop("name")
except KeyError:
name = default_logname
self._logger = logmuse.init_logger(name, **kwds)
self.debug("Logger set with logmuse.init_logger")
else:
logger_kwargs.setdefault("name", default_logname)
try:
self._logger = logmuse.logger_via_cli(args)
self.debug("Logger set with logmuse.logger_via_cli")
except logmuse.est.AbsentOptionException:
self._logger = logmuse.init_logger("pypiper", level="DEBUG")
self.debug("logger_via_cli failed; Logger set with logmuse.init_logger")
# Keep track of an ID for the number of processes attempted
self.proc_count = 0
# We use this memory to pass a memory limit to processes like java that
# can take a memory limit, so they don't get killed by a SLURM (or other
# cluster manager) overage. However, with java, the -Xmx argument can only
from ._version import __version__
import logmuse
logmuse.init_logger("refgenie")
if not args:
# strict is only for logger_via_cli.
kwds = {k: v for k, v in logger_kwargs.items() if k != "strict"}
try:
name = kwds.pop("name")
except KeyError:
name = default_logname
self._logger = logmuse.init_logger(name, **kwds)
self.debug("Logger set with logmuse.init_logger")
else:
logger_kwargs.setdefault("name", default_logname)
try:
self._logger = logmuse.logger_via_cli(args)
self.debug("Logger set with logmuse.logger_via_cli")
except logmuse.est.AbsentOptionException:
self._logger = logmuse.init_logger("pypiper", level="DEBUG")
self.debug("logger_via_cli failed; Logger set with logmuse.init_logger")
# Keep track of an ID for the number of processes attempted
self.proc_count = 0
# We use this memory to pass a memory limit to processes like java that
# can take a memory limit, so they don't get killed by a SLURM (or other
# cluster manager) overage. However, with java, the -Xmx argument can only
# limit the *heap* space, not total memory use; so occasionally SLURM will
# still kill these processes because total memory goes over the limit.
# As a kind of hack, we'll set the java processes heap limit to 95% of the
# total memory limit provided.
# This will give a little breathing room for non-heap java memory use.
if not params['mem'].endswith(('K','M','G','T')):
self.mem = params['mem'] + "M"