def registerCustomExecutables(self, workflow=None):
"""
2013.1.28
"""
AbstractVervetAlignmentWorkflow.registerCustomExecutables(self, workflow=workflow)
if workflow is None:
workflow = self
namespace = workflow.namespace
version = workflow.version
operatingSystem = workflow.operatingSystem
architecture = workflow.architecture
site_handler = workflow.site_handler
vervetSrcPath = self.vervetSrcPath
#2012.8.7 each cell is a tuple of (executable, clusterSizeMultipler (0 if u do not need clustering)
executableClusterSizeMultiplierList = []
psmc = Executable(namespace=namespace, name="psmc", version=version, \
os=operatingSystem, arch=architecture, installed=True)
psmc.addPFN(PFN("file://" + os.path.join(self.psmcFolderPath, "psmc"), site_handler))
executableClusterSizeMultiplierList.append((psmc, 0.1))
fq2psmcfa = Executable(namespace=namespace, name="fq2psmcfa", version=version, \
os=operatingSystem, arch=architecture, installed=True)
fq2psmcfa.addPFN(PFN("file://" + os.path.join(self.pymodulePath, "popgen/fq2psmcfa.sh"), site_handler))
executableClusterSizeMultiplierList.append((fq2psmcfa, 1))
psmc2history = Executable(namespace=namespace, name="psmc2history", version=version, \
os=operatingSystem, arch=architecture, installed=True)
psmc2history.addPFN(PFN("file://" + os.path.join(self.psmcFolderPath, "utils/psmc2history.pl"), site_handler))
executableClusterSizeMultiplierList.append((psmc2history, 1))
history2ms = Executable(namespace=namespace, name="history2ms", version=version, \
os=operatingSystem, arch=architecture, installed=True)
history2ms.addPFN(PFN("file://" + os.path.join(self.psmcFolderPath, "utils/history2ms.pl"), site_handler))
executableClusterSizeMultiplierList.append((history2ms, 1))
psmc_plot = Executable(namespace=namespace, name="psmc_plot", version=version, \
os=operatingSystem, arch=architecture, installed=True)
psmc_plot.addPFN(PFN("file://" + os.path.join(self.psmcFolderPath, "utils/psmc_plot.pl"), site_handler))
executableClusterSizeMultiplierList.append((psmc_plot, 1))
self.addExecutableAndAssignProperClusterSize(executableClusterSizeMultiplierList, defaultClustersSize=self.clusters_size)
self.addOneExecutableFromPathAndAssignProperClusterSize(path=os.path.join(self.pymodulePath, 'popgen/GenerateMSCommandFromPSMCOutput.sh'), \
name='GenerateMSCommandFromPSMCOutput', clusterSizeMultipler=1)
self.addOneExecutableFromPathAndAssignProperClusterSize(path=os.path.join(self.pymodulePath, 'popgen/ReplaceMSPathInMSCommandFile.py'), \
name='ReplaceMSPathInMSCommandFile', clusterSizeMultipler=2)
self.addOneExecutableFromPathAndAssignProperClusterSize(path=os.path.join(self.vervetSrcPath, 'db/input/AddIndividualAlignmentConsensusSequence2DB.py'), \
name='AddIndividualAlignmentConsensusSequence2DB', clusterSizeMultipler=0.05)
#2013.2.10 reduce clustering size for runShellCommand because ms takes a while
self.setOrChangeExecutableClusterSize(executable=self.runShellCommand, clusterSizeMultipler=0.1)
#2013.2.15 this SelectChromosomeSequences does it only on one alignment at a time
self.setOrChangeExecutableClusterSize(executable=self.SelectChromosomeSequences, clusterSizeMultipler=0.05)
def __init__(self, **keywords): """ 2013.1.25 """ AbstractVervetAlignmentWorkflow.__init__(self, **keywords) if hasattr(self, 'psmcFolderPath'): self.psmcFolderPath = self.insertHomePath(self.psmcFolderPath, self.home_path) else: self.psmcFolderPath = None if hasattr(self, 'msPath'): self.msPath = self.insertHomePath(self.msPath, self.home_path) else: self.msPath = None
