def registerCustomExecutables(self, workflow=None): """ 2011-11-25 split out of run() """ InspectAlignmentPipeline.registerCustomExecutables(self, workflow=workflow) namespace = self.namespace version = self.version operatingSystem = self.operatingSystem architecture = self.architecture clusters_size = self.clusters_size site_handler = self.site_handler executableClusterSizeMultiplierList = [] #2012.8.7 each cell is a tuple of (executable, clusterSizeMultipler (0 if u do not need clustering) verifyBamID = Executable(namespace=namespace, name="verifyBamID", version=version, os=operatingSystem,\ arch=architecture, installed=True) verifyBamID.addPFN(PFN("file://" + self.verifyBamIDPath, site_handler)) executableClusterSizeMultiplierList.append((verifyBamID, 1)) self.addExecutableAndAssignProperClusterSize(executableClusterSizeMultiplierList, defaultClustersSize=self.clusters_size)
def __init__(self, **keywords): """ 2011-11-4 """ self.pathToInsertHomePathList.append('verifyBamIDPath') InspectAlignmentPipeline.__init__(self, **keywords)