def registerCustomExecutables(self, workflow=None):
"""
2012.3.14
"""
if workflow is None:
workflow = self
AbstractVervetWorkflow.registerCustomExecutables(self, workflow=workflow)
self.addOneExecutableFromPathAndAssignProperClusterSize(
path=os.path.join(self.vervetSrcPath, "mapper/CountFastqReadBaseCount.py"),
name="CountFastqReadBaseCount",
clusterSizeMultipler=1,
)
self.addOneExecutableFromPathAndAssignProperClusterSize(
path=os.path.join(self.vervetSrcPath, "db/input/PutReadBaseCountIntoDB.py"),
name="PutReadBaseCountIntoDB",
clusterSizeMultipler=0.2,
)
def registerCustomExecutables(self, workflow=None):
"""
2011-11-28
"""
if workflow==None:
workflow=self
AbstractVervetWorkflow.registerCustomExecutables(self, workflow)
namespace = workflow.namespace
version = workflow.version
operatingSystem = workflow.operatingSystem
architecture = workflow.architecture
clusters_size = workflow.clusters_size
site_handler = workflow.site_handler
vervetSrcPath = self.vervetSrcPath
executableClusterSizeMultiplierList = [] #2012.8.7 each cell is a tuple of (executable, clusterSizeMultipler (0 if u do not need clustering)
AggregateAndHClusterDistanceMatrix = Executable(namespace=namespace, name="AggregateAndHClusterDistanceMatrix", \
version=version, \
os=operatingSystem, arch=architecture, installed=True)
AggregateAndHClusterDistanceMatrix.addPFN(PFN("file://" + os.path.join(vervetSrcPath, "reducer/AggregateAndHClusterDistanceMatrix.py"), \
site_handler))
executableClusterSizeMultiplierList.append((AggregateAndHClusterDistanceMatrix, 0))
self.addExecutableAndAssignProperClusterSize(executableClusterSizeMultiplierList, defaultClustersSize=self.clusters_size)
