def merge_sample_alignments(args): sample_name = args.sampleName mate_handler = MateHandler() sample = mate_handler.get_sample_by_name(sample_name) sp = SamplePipeline(sample) pipeline_handler = PipelineHandler(sp, ncores=22, memory=220000, clean_output_dir=True) pipeline_handler.run_on_condor()
def align_sample(args): sample_name = args.sampleName mate_handler = MateHandler() sample = mate_handler.get_sample_by_name(sample_name) ## conditionally, submit all the samples directly to condor (remove in the future) for mate in sample.mates: pipeline = MatePipeline(mate) pipeline.setup() pipeline_handler = PipelineHandler(pipeline, ncores=10, memory=10900) pipeline_handler.run_on_condor()
def submit(self): for mate in self.list_mates_to_align(): pipeline = MatePipeline(mate) submitter = PipelineHandler(pipeline, self.ncores, self.memory) submitter.run_on_condor() self.condor_logs.append(submitter.get_condor_log())