def updateProject(path):
mcProj = MultiCactusProject()
mcProj.readXML(path)
basePath, name = os.path.split(path)
for name,oldPath in mcProj.expMap.items():
fileName = os.path.basename(oldPath)
dirName = os.path.dirname(oldPath).rpartition('/')[2]
newPath = os.path.join(basePath, dirName, fileName)
if not os.path.isfile(newPath):
raise RuntimeError("Experiment file %s not found\n" % newPath)
mcProj.expMap[name] = newPath
exp = ExperimentWrapper(ET.parse(newPath).getroot())
oldDbDir = exp.getDbDir()
if oldDbDir is not None:
dbDirName = oldDbDir[oldDbDir.find(name):]
newDbDir = os.path.join(basePath, dbDirName)
exp.setDbDir(newDbDir)
oldRefPath = exp.getReferencePath()
if oldRefPath is not None:
refName = oldRefPath[oldRefPath.find(name):]
newRefPath = os.path.join(basePath, refName)
exp.setReferencePath(newRefPath)
oldHalPath = exp.getHALPath()
if oldHalPath is not None:
halName = oldHalPath[oldHalPath.find(name):]
newHalPath = os.path.join(basePath, halName)
exp.setHALPath(newHalPath)
oldHalFastaPath = exp.getHALFastaPath()
if oldHalFastaPath is not None:
halFastaName = oldHalFastaPath[oldHalFastaPath.find(name):]
newHalFastaPath = os.path.join(basePath, halFastaName)
exp.setHALFastaPath(newHalFastaPath)
# seems to have dissappeared from experiment?
#oldMafPath = exp.getMAFPath()
#if oldMafPath is not None:
# mafName = oldMafPath[oldMafPath.find(name):]
# newMafPath = os.path.join(basePath, mafName)
# exp.setMAFPath(newMafPath)
if exp.getDbType() == "kyoto_tycoon":
oldHostName = exp.getDbHost()
if oldHostName is not None:
newHostName = socket.gethostname()
exp.setDbHost(newHostName)
system("cp %s %s.old" %(newPath, newPath))
exp.writeXML(newPath)
mcProj.writeXML(path)
def run(self):
logger.info("Progressive Up: " + self.event)
# open up the experiment
# note that we copy the path into the options here
self.options.experimentFile = self.project.expMap[self.event]
expXml = ET.parse(self.options.experimentFile).getroot()
experiment = ExperimentWrapper(expXml)
configXml = ET.parse(experiment.getConfigPath()).getroot()
configWrapper = ConfigWrapper(configXml)
# need at least 3 processes for every event when using ktserver:
# 1 proc to run jobs, 1 proc to run server, 1 proc to run 2ndary server
if experiment.getDbType() == "kyoto_tycoon":
maxParallel = min(len(self.project.expMap),
configWrapper.getMaxParallelSubtrees())
if self.options.batchSystem == "singleMachine":
if int(self.options.maxThreads) < maxParallel * 3:
raise RuntimeError("At least %d threads are required (only %d were specified) to handle up to %d events using kyoto tycoon. Either increase the number of threads using the --maxThreads option or decrease the number of parallel jobs (currently %d) by adjusting max_parallel_subtrees in the config file" % (maxParallel * 3, self.options.maxThreads, maxParallel, configWrapper.getMaxParallelSubtrees()))
else:
if int(self.options.maxCpus) < maxParallel * 3:
raise RuntimeError("At least %d concurrent cpus are required to handle up to %d events using kyoto tycoon. Either increase the number of cpus using the --maxCpus option or decrease the number of parallel jobs (currently %d) by adjusting max_parallel_subtrees in the config file" % (maxParallel * 3, maxParallel, configWrapper.getMaxParallelSubtrees()))
# take union of command line options and config options for hal and reference
if self.options.buildReference == False:
refNode = findRequiredNode(configXml, "reference")
self.options.buildReference = getOptionalAttrib(refNode, "buildReference", bool, False)
halNode = findRequiredNode(configXml, "hal")
if self.options.buildHal == False:
self.options.buildHal = getOptionalAttrib(halNode, "buildHal", bool, False)
if self.options.buildFasta == False:
self.options.buildFasta = getOptionalAttrib(halNode, "buildFasta", bool, False)
# get parameters that cactus_workflow stuff wants
workFlowArgs = CactusWorkflowArguments(self.options)
# copy over the options so we don't trail them around
workFlowArgs.buildReference = self.options.buildReference
workFlowArgs.buildHal = self.options.buildHal
workFlowArgs.buildFasta = self.options.buildFasta
workFlowArgs.overwrite = self.options.overwrite
workFlowArgs.globalLeafEventSet = self.options.globalLeafEventSet
experiment = ExperimentWrapper(workFlowArgs.experimentNode)
donePath = os.path.join(os.path.dirname(workFlowArgs.experimentFile), "DONE")
doneDone = os.path.isfile(donePath)
refDone = not workFlowArgs.buildReference or os.path.isfile(experiment.getReferencePath())
halDone = not workFlowArgs.buildHal or (os.path.isfile(experiment.getHALFastaPath()) and
os.path.isfile(experiment.getHALPath()))
if not workFlowArgs.overwrite and doneDone and refDone and halDone:
self.logToMaster("Skipping %s because it is already done and overwrite is disabled" %
self.event)
else:
system("rm -f %s" % donePath)
# delete database
# and overwrite specified (or if reference not present)
dbPath = os.path.join(experiment.getDbDir(),
experiment.getDbName())
seqPath = os.path.join(experiment.getDbDir(), "sequences")
system("rm -f %s* %s %s" % (dbPath, seqPath,
experiment.getReferencePath()))
if workFlowArgs.configWrapper.getDoTrimStrategy() and workFlowArgs.outgroupEventNames is not None:
# Use the trimming strategy to blast ingroups vs outgroups.
self.addChildTarget(CactusTrimmingBlastPhase(cactusWorkflowArguments=workFlowArgs, phaseName="trimBlast"))
else:
self.addChildTarget(CactusSetupPhase(cactusWorkflowArguments=workFlowArgs,
phaseName="setup"))
logger.info("Going to create alignments and define the cactus tree")
self.setFollowOnTarget(FinishUp(workFlowArgs, self.project))