def setup(self):
# internal management classes
self.vMonitor = RRDVermontMonitor(self.xpaths, self.names, self.moninterval)
self.rInterface = RemoteInterface(self.dir, self.cfgfile, self.logfile, self.vMonitor, self.names)
# RPC server
self.server = VCRPCServer((self.bindAddress, self.listenPort), allow_none=True, logRequests=False)
self.server.allow_reuse_address = True
self.server.allowedIp = self.allowedIp #IGNORE:W0201
self.server.register_instance(self.rInterface)
import DatabaseModel
from config import SSH_HOST
import config
# The host to which the computer is connected need to be recognized with the pem keys!!
# How to run this script:
# PYTHONPATH='.' luigi --module luigi_pipeline AnnotateAlignment --pid 1 --sid 4 --input /Volumes/data/dev/nanopore/pipeline/storage/rawreads.fasta --barcode /Volumes/data/dev/nanopore/pipeline/storage/barcodes.fasta
remote_storage_root = config.remote_storage
# Get the parameters stored in the database using the given sample id.
parameters = DatabaseModel.parameters()
report = DatabaseModel.status()
results = DatabaseModel.Results()
remoteInterface = RemoteInterface()
######################################################################################################################################
######################################################################################################################################
class CreateEnv(luigi.Task):
stage = 'CREATING ENVIRONMENT IN CLUSTER'
def output(self):
parameters.setParameters(parameters.data)
status = RemoteTarget(parameters.data['remote_storage'], SSH_HOST)
# if status: stage.pushStatus(parameters.data['id'], stage.CreateEnv)
return status
def run(self):
