class RunCactusPreprocessorThenProgressiveDown2(RoundedJob):
def __init__(self, options, project, event, schedule, memory=None, cores=None):
RoundedJob.__init__(self, memory=memory, cores=cores, preemptable=True)
self.options = options
self.project = project
self.event = event
self.schedule = schedule
def run(self, fileStore):
self.configNode = ET.parse(fileStore.readGlobalFile(self.project.getConfigID())).getroot()
self.configWrapper = ConfigWrapper(self.configNode)
self.configWrapper.substituteAllPredefinedConstantsWithLiterals()
# Save preprocessed sequences
if self.options.intermediateResultsUrl is not None:
preprocessedSequences = self.project.getOutputSequenceIDMap()
for genome, seqID in preprocessedSequences.items():
fileStore.exportFile(seqID, self.options.intermediateResultsUrl + '-preprocessed-' + genome)
# Log the stats for the preprocessed assemblies
for name, sequence in self.project.getOutputSequenceIDMap().items():
self.addChildJobFn(logAssemblyStats, "After preprocessing", name, sequence)
project = self.addChild(ProgressiveDown(options=self.options, project=self.project, event=self.event, schedule=self.schedule, memory=self.configWrapper.getDefaultMemory())).rv()
#Combine the smaller HAL files from each experiment
return self.addFollowOnJobFn(exportHal, project=project, memory=self.configWrapper.getDefaultMemory(),
disk=self.configWrapper.getExportHalDisk(),
preemptable=False).rv()
class RunCactusPreprocessorThenProgressiveDown2(RoundedJob):
def __init__(self, options, project, event, schedule, memory=None, cores=None):
RoundedJob.__init__(self, memory=memory, cores=cores, preemptable=True)
self.options = options
self.project = project
self.event = event
self.schedule = schedule
def run(self, fileStore):
self.configNode = ET.parse(fileStore.readGlobalFile(self.project.getConfigID())).getroot()
self.configWrapper = ConfigWrapper(self.configNode)
self.configWrapper.substituteAllPredefinedConstantsWithLiterals()
# Save preprocessed sequences
if self.options.intermediateResultsUrl is not None:
preprocessedSequences = self.project.getOutputSequenceIDMap()
for genome, seqID in preprocessedSequences.items():
fileStore.exportFile(seqID, self.options.intermediateResultsUrl + '-preprocessed-' + genome)
# Log the stats for the preprocessed assemblies
for name, sequence in self.project.getOutputSequenceIDMap().items():
self.addChildJobFn(logAssemblyStats, "After preprocessing", name, sequence)
project = self.addChild(ProgressiveDown(options=self.options, project=self.project, event=self.event, schedule=self.schedule, memory=self.configWrapper.getDefaultMemory())).rv()
#Combine the smaller HAL files from each experiment
return self.addFollowOnJobFn(exportHal, project=project, memory=self.configWrapper.getDefaultMemory(),
disk=self.configWrapper.getExportHalDisk(),
preemptable=False).rv()
