Python PipelineHandler Examples

Example #1

File: merge_sample_alignments.py Project: petr-volkov/easy-wgbs

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()

Example #2

File: align_sample.py Project: petr-volkov/easy-wgbs

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()

Example #3

File: condor_project.py Project: petr-volkov/easy-wgbs

 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())