def main(args): options = parse_args(args) RealTimeLogger.start_master() filtered_gams = [] skip_words = options.skip.split(",") for gam in options.in_gams: skip_gam = False for word in skip_words: if len(word) > 0 and word in gam: skip_gam = True if not skip_gam: filtered_gams.append(gam) options.in_gams = filtered_gams for gam in options.in_gams: if len(gam.split("/")) < 3 or os.path.splitext(gam)[1] != ".gam": raise RuntimeError("Input gam paths must be of the form " ".../<alg>/<reads>/<filename>.gam") # Make a root job root_job = Job.wrapJobFn(call_variants, options, cores=1, memory="2G", disk="2G") # Run it and see how many jobs fail failed_jobs = Job.Runner.startToil(root_job, options) if failed_jobs > 0: raise Exception("{} jobs failed!".format(failed_jobs)) RealTimeLogger.stop_master()
def main(args): options = parse_args(args) RealTimeLogger.start_master() for gam in options.in_gams: if len(gam.split("/")) < 3 or os.path.splitext(gam)[1] != ".gam": raise RuntimeError("Input gam paths must be of the form " ".../<alg>/<reads>/<filename>.gam") robust_makedirs(json_out_path(options)) robust_makedirs(compare_out_path(options)) # Make a root job root_job = Job.wrapJobFn(compute_all_indexes, options, cores=1, memory="2G", disk=0) # Run it and see how many jobs fail if not options.only_summary: failed_jobs = Job.Runner.startToil(root_job, options) else: failed_jobs = 0 if failed_jobs > 0: raise Exception("{} jobs failed!".format(failed_jobs)) RealTimeLogger.stop_master() # make some tables from the json comparison output #dist_table(options) #acc_table(options) snp_count_table(options) graph_size_table(options)
def main(args): options = parse_args(args) RealTimeLogger.start_master() filtered_gams = [] skip_words = options.skip.split(",") for gam in options.in_gams: skip_gam = False for word in skip_words: if len(word) > 0 and word in gam: skip_gam = True if not skip_gam: filtered_gams.append(gam) options.in_gams = filtered_gams for gam in options.in_gams: if len(gam.split("/")) < 3 or os.path.splitext(gam)[1] != ".gam": raise RuntimeError("Input gam paths must be of the form " ".../<alg>/<reads>/<filename>.gam") # Make a root job root_job = Job.wrapJobFn(call_variants, options, cores=1, memory="2G", disk="2G") # Run it and see how many jobs fail failed_jobs = Job.Runner.startToil(root_job, options) if failed_jobs > 0: raise Exception("{} jobs failed!".format(failed_jobs)) RealTimeLogger.stop_master()
def main(args): options = parse_args(args) RealTimeLogger.start_master() for graph in options.graphs: if os.path.splitext(graph)[1] != ".vg": raise RuntimeError("Input graphs expected to have .vg extension") # Make a root job root_job = Job.wrapJobFn(compute_kmer_indexes, options, cores=1, memory="2G", disk=0) # Run it and see how many jobs fail if not options.only_summary: failed_jobs = Job.Runner.startToil(root_job, options) else: failed_jobs = 0 if failed_jobs > 0: raise Exception("{} jobs failed!".format(failed_jobs)) RealTimeLogger.stop_master() # Do the drawing outside toil to get around weird import problems cluster_comparisons(options)
def main(args): options = parse_args(args) RealTimeLogger.start_master() # Make a root job root_job = Job.wrapJobFn(run_and_evaluate, options, cores=1, memory="2G", disk="2G") # Run it and get the return value answer = Job.Runner.startToil(root_job, options) RealTimeLogger.stop_master() print("Root return value:") print(answer)