def run(self, fileStore):
sequenceFiles1 = [
fileStore.readGlobalFile(fileID)
for fileID in self.sequenceFileIDs1
]
if self.blastOptions.gpuLastz == True:
# wga-gpu has a 3G limit.
self.blastOptions.chunkSize = 3000000000
chunks = runGetChunks(
sequenceFiles=sequenceFiles1,
chunksDir=getTempDirectory(rootDir=fileStore.getLocalTempDir()),
chunkSize=self.blastOptions.chunkSize,
overlapSize=self.blastOptions.overlapSize)
if len(chunks) == 0:
raise Exception(
"no chunks produced for files: {} ".format(sequenceFiles1))
logger.info(
"Broken up the sequence files into individual 'chunk' files")
chunkIDs = [
fileStore.writeGlobalFile(chunk, cleanup=True) for chunk in chunks
]
diagonalResultsID = self.addChild(
MakeSelfBlasts(self.blastOptions, chunkIDs)).rv()
offDiagonalResultsID = self.addChild(
MakeOffDiagonalBlasts(self.blastOptions, chunkIDs)).rv()
logger.debug("Collating the blasts after blasting all-against-all")
return self.addFollowOn(
CollateBlasts(self.blastOptions,
[diagonalResultsID, offDiagonalResultsID])).rv()
def run(self, fileStore):
sequenceFiles1 = [
fileStore.readGlobalFile(fileID)
for fileID in self.sequenceFileIDs1
]
chunks = runGetChunks(
sequenceFiles=sequenceFiles1,
chunksDir=getTempDirectory(rootDir=fileStore.getLocalTempDir()),
chunkSize=self.blastOptions.chunkSize,
overlapSize=self.blastOptions.overlapSize)
assert len(chunks) > 0
logger.info(
"Broken up the sequence files into individual 'chunk' files")
chunkIDs = [
fileStore.writeGlobalFile(chunk, cleanup=True) for chunk in chunks
]
diagonalResultsID = self.addChild(
MakeSelfBlasts(self.blastOptions, chunkIDs)).rv()
offDiagonalResultsID = self.addChild(
MakeOffDiagonalBlasts(self.blastOptions, chunkIDs)).rv()
logger.debug("Collating the blasts after blasting all-against-all")
return self.addFollowOn(
CollateBlasts(self.blastOptions,
[diagonalResultsID, offDiagonalResultsID])).rv()
def run(self, fileStore):
sequenceFiles1 = [fileStore.readGlobalFile(fileID) for fileID in self.sequenceFileIDs1]
chunks = runGetChunks(sequenceFiles=sequenceFiles1, chunksDir=getTempDirectory(rootDir=fileStore.getLocalTempDir()), chunkSize = self.blastOptions.chunkSize, overlapSize=self.blastOptions.overlapSize)
assert len(chunks) > 0
logger.info("Broken up the sequence files into individual 'chunk' files")
chunkIDs = [fileStore.writeGlobalFile(chunk, cleanup=True) for chunk in chunks]
diagonalResultsID = self.addChild(MakeSelfBlasts(self.blastOptions, chunkIDs)).rv()
offDiagonalResultsID = self.addChild(MakeOffDiagonalBlasts(self.blastOptions, chunkIDs)).rv()
logger.debug("Collating the blasts after blasting all-against-all")
return self.addFollowOn(CollateBlasts(self.blastOptions, [diagonalResultsID, offDiagonalResultsID])).rv()
def run(self, fileStore):
logger.info("Chunk IDs: %s" % self.chunkIDs)
#Avoid compression if just one chunk
self.blastOptions.compressFiles = self.blastOptions.compressFiles and len(self.chunkIDs) > 2
resultsIDs = []
for i in range(len(self.chunkIDs)):
resultsIDs.append(self.addChild(RunSelfBlast(self.blastOptions, self.chunkIDs[i])).rv())
logger.info("Made the list of self blasts")
#Setup job to make all-against-all blasts
logger.debug("Collating self blasts.")
logger.info("Blast file IDs: %s" % resultsIDs)
return self.addFollowOn(CollateBlasts(self.blastOptions, resultsIDs)).rv()
def run(self, fileStore):
logger.info("Chunk IDs: %s" % self.chunkIDs)
#Avoid compression if just one chunk
self.blastOptions.compressFiles = self.blastOptions.compressFiles and len(self.chunkIDs) > 2
resultsIDs = []
for i in xrange(len(self.chunkIDs)):
resultsIDs.append(self.addChild(RunSelfBlast(self.blastOptions, self.chunkIDs[i])).rv())
logger.info("Made the list of self blasts")
#Setup job to make all-against-all blasts
logger.debug("Collating self blasts.")
logger.info("Blast file IDs: %s" % resultsIDs)
return self.addFollowOn(CollateBlasts(self.blastOptions, resultsIDs)).rv()
def findOccupiedPorts():
"""Attempt to find all currently taken TCP ports.
Returns a set of ints, representing taken ports."""
netstatOutput = cactus_call(parameters=["netstat", "-tuplen"], check_output=True)
ports = set()
for line in netstatOutput.split("\n"):
fields = line.split()
if len(fields) != 9:
# Header or other garbage line
continue
port = int(fields[3].split(':')[-1])
ports.add(port)
logger.debug('Detected ports in use: %s' % repr(ports))
return ports
