def run(self, fileStore):
chunkList = [readGlobalFileWithoutCache(fileStore, fileID) for fileID in self.chunkIDList]
#Docker expects paths relative to the work dir
chunkList = [os.path.basename(chunk) for chunk in chunkList]
outSequencePath = fileStore.getLocalTempFile()
cactus_call(outfile=outSequencePath, stdin_string=" ".join(chunkList),
parameters=["cactus_batch_mergeChunks"])
return fileStore.writeGlobalFile(outSequencePath)
def run(self, fileStore):
chunkList = [readGlobalFileWithoutCache(fileStore, fileID) for fileID in self.chunkIDList]
#Docker expects paths relative to the work dir
chunkList = [os.path.basename(chunk) for chunk in chunkList]
outSequencePath = fileStore.getLocalTempFile()
cactus_call(outfile=outSequencePath, stdin_string=" ".join(chunkList),
parameters=["cactus_batch_mergeChunks"])
return fileStore.writeGlobalFile(outSequencePath)
def run(self, fileStore):
logger.info("Results IDs: %s" % self.resultsFileIDs)
resultsFiles = [readGlobalFileWithoutCache(fileStore, fileID) for fileID in self.resultsFileIDs]
collatedResultsFile = fileStore.getLocalTempFile()
catFiles(resultsFiles, collatedResultsFile)
logger.info("Collated the alignments to the file: %s", collatedResultsFile)
collatedResultsID = fileStore.writeGlobalFile(collatedResultsFile)
for resultsFileID in self.resultsFileIDs:
fileStore.deleteGlobalFile(resultsFileID)
return collatedResultsID
def run(self, fileStore):
logger.info("Results IDs: %s" % self.resultsFileIDs)
resultsFiles = [readGlobalFileWithoutCache(fileStore, fileID) for fileID in self.resultsFileIDs]
collatedResultsFile = fileStore.getLocalTempFile()
catFiles(resultsFiles, collatedResultsFile)
logger.info("Collated the alignments to the file: %s", collatedResultsFile)
collatedResultsID = fileStore.writeGlobalFile(collatedResultsFile)
for resultsFileID in self.resultsFileIDs:
fileStore.deleteGlobalFile(resultsFileID)
return collatedResultsID
def run(self, fileStore):
logger.info("Results IDs: %s" % self.resultsFileIDs)
resultsFiles = [
readGlobalFileWithoutCache(fileStore, fileID)
for fileID in self.resultsFileIDs
]
collatedResultsFile = fileStore.getLocalTempFile()
catFiles(resultsFiles, collatedResultsFile)
logger.info("Collated the alignments to the file: %s",
collatedResultsFile)
collatedResultsID = fileStore.writeGlobalFile(collatedResultsFile)
for i in range(0, len(self.resultsFileIDs), self.delete_batch_size):
self.addChild(
DeleteFileIDs(self.resultsFileIDs[i:i +
self.delete_batch_size]))
return collatedResultsID