def writeXml(self):
assert os.path.isdir(self.workingDir)
configPath = absSymPath(
os.path.join(self.workingDir, "config.xml"))
expPath = absSymPath(
os.path.join(self.workingDir, "expTemplate.xml"))
self.expWrapper.setConfigPath(configPath)
self.configWrapper.writeXML(configPath)
self.expWrapper.writeXML(expPath)
projPath = os.path.join(self.workingDir,
ProjectWrapper.alignmentDirName)
if os.path.exists(projPath) and self.options.overwrite:
system("rm -rf %s" % projPath)
if self.options.outputMaf is True:
fixNames=1
else:
fixNames=0
if os.path.exists(projPath):
if not self.isSameAsExisting(expPath, projPath, fixNames):
raise RuntimeError("Existing project %s not " % projPath+
"compatible with current input. Please "
"erase the working directory or rerun "
"with the --overwrite option to start "
"from scratch.")
else:
logPath = os.path.join(self.workingDir, 'cactus.log')
logFile = open(logPath, "a")
logFile.write("\nContinuing existing alignment. Use "
"--overwrite or erase the working directory to "
"force restart from scratch.\n")
logFile.close()
else:
cmd = "cactus_createMultiCactusProject.py \"%s\" \"%s\" --fixNames=%d" % (
expPath, projPath, fixNames)
if len(self.seqFile.outgroups) > 0:
cmd += " --outgroupNames " + ",".join(self.seqFile.outgroups)
if self.options.rootOutgroupDists:
cmd += " --rootOutgroupDists %s" % self.options.rootOutgroupDists
cmd += " --rootOutgroupPaths %s" % self.options.rootOutgroupPaths
if self.options.root is not None:
cmd += " --root %s" % self.options.root
system(cmd)
def writeXml(self):
assert os.path.isdir(self.workingDir)
configPath = absSymPath(os.path.join(self.workingDir, "config.xml"))
expPath = absSymPath(os.path.join(self.workingDir, "expTemplate.xml"))
self.expWrapper.setConfigPath(configPath)
self.configWrapper.writeXML(configPath)
self.expWrapper.writeXML(expPath)
projPath = os.path.join(self.workingDir,
ProjectWrapper.alignmentDirName)
if len(self.seqFile.outgroups) == 0:
# No outgroups specified, assume the default outgroup set
outgroups = None
else:
outgroups = self.seqFile.outgroups
runCreateMultiCactusProject(expPath,
projPath,
outgroupNames=outgroups,
root=self.options.root)
def writeXml(self):
assert os.path.isdir(self.workingDir)
configPath = absSymPath(
os.path.join(self.workingDir, "config.xml"))
expPath = absSymPath(
os.path.join(self.workingDir, "expTemplate.xml"))
self.expWrapper.setConfigPath(configPath)
self.configWrapper.writeXML(configPath)
self.expWrapper.writeXML(expPath)
projPath = os.path.join(self.workingDir,
ProjectWrapper.alignmentDirName)
if len(self.seqFile.outgroups) == 0:
# No outgroups specified, assume the default outgroup set
outgroups = None
else:
outgroups = self.seqFile.outgroups
runCreateMultiCactusProject(expPath, projPath, fixNames=0,
outgroupNames=outgroups,
root=self.options.root)
def toXMLElement(self):
assert self.tree is not None
elem = ET.Element("cactus_workflow_experiment")
seqString = ""
for node in self.tree.postOrderTraversal():
if self.tree.isLeaf(node):
name = self.tree.getName(node)
path = self.pathMap[name]
path.replace(" ", "\ ")
seqString += absSymPath(path) + " "
elem.attrib["sequences"] = seqString
elem.attrib["species_tree"] = NXNewick().writeString(self.tree)
elem.attrib["config"] = "defaultProgressive"
return elem
def toXMLElement(self):
assert self.tree is not None
elem = ET.Element("cactus_workflow_experiment")
seqString = ""
for node in self.tree.postOrderTraversal():
if self.tree.isLeaf(node):
name = self.tree.getName(node)
path = self.pathMap[name]
path.replace(" ", "\ ")
seqString += absSymPath(path) + " "
elem.attrib["sequences"] = seqString
elem.attrib["species_tree"] = NXNewick().writeString(self.tree)
elem.attrib["config"] = "defaultProgressive"
return elem
def startJobTree(self, options):
"""Runs jobtree using the given options (see Stack.getDefaultOptions
and Stack.addJobTreeOptions).
"""
self.verifyJobTreeOptions(options)
setLoggingFromOptions(options)
options.jobTree = absSymPath(options.jobTree)
if os.path.isdir(options.jobTree):
config, batchSystem = reloadJobTree(options.jobTree)
else:
config, batchSystem = createJobTree(options)
#Setup first job.
command = self.makeRunnable(options.jobTree)
memory = self.getMemory()
cpu = self.getCpu()
createFirstJob(command, config, memory=memory, cpu=cpu)
loadEnvironment(config)
return mainLoop(config, batchSystem)
def startJobTree(self, options):
"""Runs jobtree using the given options (see Stack.getDefaultOptions
and Stack.addJobTreeOptions).
"""
self.verifyJobTreeOptions(options)
setLoggingFromOptions(options)
options.jobTree = absSymPath(options.jobTree)
if os.path.isdir(options.jobTree):
config, batchSystem = reloadJobTree(options.jobTree)
else:
config, batchSystem = createJobTree(options)
#Setup first job.
command = self.makeRunnable(options.jobTree)
memory = self.getMemory()
cpu = self.getCpu()
createFirstJob(command, config, memory=memory, cpu=cpu)
loadEnvironment(config)
return mainLoop(config, batchSystem)
def createJobTree(options):
logger.info("Starting to create the job tree setup for the first time")
options.jobTree = absSymPath(options.jobTree)
os.mkdir(options.jobTree)
os.mkdir(getJobFileDirName(options.jobTree))
config = ET.Element("config")
config.attrib["log_level"] = getLogLevelString()
config.attrib["job_tree"] = options.jobTree
config.attrib["parasol_command"] = options.parasolCommand
config.attrib["try_count"] = str(int(options.retryCount) + 1)
config.attrib["max_job_duration"] = str(float(options.maxJobDuration))
config.attrib["batch_system"] = options.batchSystem
config.attrib["job_time"] = str(float(options.jobTime))
config.attrib["max_log_file_size"] = str(int(options.maxLogFileSize))
config.attrib["default_memory"] = str(int(options.defaultMemory))
config.attrib["default_cpu"] = str(int(options.defaultCpu))
config.attrib["max_cpus"] = str(int(options.maxCpus))
config.attrib["max_memory"] = str(int(options.maxMemory))
config.attrib["max_threads"] = str(int(options.maxThreads))
if options.bigBatchSystem != None:
config.attrib["big_batch_system"] = options.bigBatchSystem
config.attrib["big_memory_threshold"] = str(
int(options.bigMemoryThreshold))
config.attrib["big_cpu_threshold"] = str(int(options.bigCpuThreshold))
config.attrib["big_max_cpus"] = str(int(options.bigMaxCpus))
config.attrib["big_max_memory"] = str(int(options.bigMaxMemory))
if options.stats:
config.attrib["stats"] = ""
#Load the batch system.
batchSystem = loadTheBatchSystem(config, options)
logger.info("Loaded the batch system %s" % batchSystem)
#Set the parameters determining the polling frequency of the system.
config.attrib["rescue_jobs_frequency"] = str(
float(batchSystem.getRescueJobFrequency()))
if options.rescueJobsFrequency != None:
config.attrib["rescue_jobs_frequency"] = str(
float(options.rescueJobsFrequency))
writeConfig(config)
logger.info("Finished the job tree setup")
return config, batchSystem
def main():
usage = "usage: %prog <project xml path>"
description = "Update the _project.xml and _experiment.xml files to use current directory structure"
parser = OptionParser(usage=usage, description=description)
options, args = parser.parse_args()
if len(args) != 1:
parser.print_help()
raise RuntimeError("Wrong number of arguments")
path = absSymPath(args[0])
if not os.path.isfile(path):
raise RuntimeError("Project file %s not found\n" % path)
system("cp %s %s.old" %(path, path))
updateProject(path)
return 0
def createJobTree(options):
logger.info("Starting to create the job tree setup for the first time")
options.jobTree = absSymPath(options.jobTree)
os.mkdir(options.jobTree)
os.mkdir(getJobFileDirName(options.jobTree))
config = ET.Element("config")
config.attrib["log_level"] = getLogLevelString()
config.attrib["job_tree"] = options.jobTree
config.attrib["parasol_command"] = options.parasolCommand
config.attrib["try_count"] = str(int(options.retryCount) + 1)
config.attrib["max_job_duration"] = str(float(options.maxJobDuration))
config.attrib["batch_system"] = options.batchSystem
config.attrib["job_time"] = str(float(options.jobTime))
config.attrib["max_log_file_size"] = str(int(options.maxLogFileSize))
config.attrib["default_memory"] = str(int(options.defaultMemory))
config.attrib["default_cpu"] = str(int(options.defaultCpu))
config.attrib["max_cpus"] = str(int(options.maxCpus))
config.attrib["max_memory"] = str(int(options.maxMemory))
config.attrib["max_threads"] = str(int(options.maxThreads))
if options.bigBatchSystem != None:
config.attrib["big_batch_system"] = options.bigBatchSystem
config.attrib["big_memory_threshold"] = str(int(options.bigMemoryThreshold))
config.attrib["big_cpu_threshold"] = str(int(options.bigCpuThreshold))
config.attrib["big_max_cpus"] = str(int(options.bigMaxCpus))
config.attrib["big_max_memory"] = str(int(options.bigMaxMemory))
if options.stats:
config.attrib["stats"] = ""
#Load the batch system.
batchSystem = loadTheBatchSystem(config)
#Set the parameters determining the polling frequency of the system.
config.attrib["rescue_jobs_frequency"] = str(float(batchSystem.getRescueJobFrequency()))
if options.rescueJobsFrequency != None:
config.attrib["rescue_jobs_frequency"] = str(float(options.rescueJobsFrequency))
writeConfig(config)
logger.info("Finished the job tree setup")
return config, batchSystem