def registerExecutables(self, workflow=None):
"""
2012.2.15
"""
AbstractWorkflow.registerExecutables(self)
namespace = self.namespace
version = self.version
operatingSystem = self.operatingSystem
architecture = self.architecture
clusters_size = self.clusters_size
site_handler = self.site_handler
variationSrcPath = self.variationSrcPath
vervetSrcPath = self.vervetSrcPath
#2012.8.7 each cell is a tuple of (executable, clusterSizeMultipler (0 if u do not need clustering)
executableClusterSizeMultiplierList = []
Stock_250kDB = Executable(namespace=namespace, name="Stock_250kDB", version=version, \
os=operatingSystem, arch=architecture, installed=True)
Stock_250kDB.addPFN(PFN("file://" + os.path.join(self.variationSrcPath, "db/Stock_250kDB.py"), site_handler))
executableClusterSizeMultiplierList.append((Stock_250kDB, 0))
self.addExecutableAndAssignProperClusterSize(executableClusterSizeMultiplierList, defaultClustersSize=self.clusters_size)
def registerCustomExecutables(self, workflow=None):
"""
2011-11-28
"""
AbstractWorkflow.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)
nucmer = Executable(namespace=namespace, name="nucmer", version=version, \
os=operatingSystem, arch=architecture, installed=True)
nucmer.addPFN(PFN("file://" + os.path.join(self.mummer_path, "nucmer"), site_handler))
executableClusterSizeMultiplierList.append((nucmer, 0))
PostNucmer = Executable(namespace=namespace, name="PostNucmer", version=version, \
os=operatingSystem, arch=architecture, installed=True)
PostNucmer.addPFN(PFN("file://" + os.path.join(vervetSrcPath, "shell/PostNucmer.sh"), site_handler))
executableClusterSizeMultiplierList.append((PostNucmer, 0))
self.addExecutableAndAssignProperClusterSize(executableClusterSizeMultiplierList, defaultClustersSize=self.clusters_size)
#2013.07.26
self.addOneExecutableFromPathAndAssignProperClusterSize(path= os.path.join(vervetSrcPath, "mapper/SelectAndSplitFastaRecords.py"), \
name='SelectAndSplitFastaRecords', clusterSizeMultipler=0)
def __init__(self, **keywords): """ 2012.2.15 """ AbstractWorkflow.__init__(self, **keywords) self.variationSrcPath = self.insertHomePath(self.variationSrcPath, self.home_path) self.tabixPath = self.insertHomePath(self.tabixPath, self.home_path) self.chr_pattern = re.compile(r'(\w+\d+).*') self.contig_id_pattern = re.compile(r'Contig(\d+).*') self.connectDB() if not self.data_dir: self.data_dir = self.db.data_dir
def __init__(self, **keywords):
"""
2011-7-11
"""
self.pathToInsertHomePathList.append('mummer_path') #inserted before AbstractWorkflow.__init__()
AbstractWorkflow.__init__(self, **keywords)