comparison runner.py @ 9:08e987868f0f draft

planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign commit 062a761a340e095ea7ef7ed7cd1d3d55b1fdc5c4

8:150de8a3954a

    if args.debug:
        print(f"estimated chunk size: {chunk_size}", file=sys.stderr, flush=True)

    with concurrent.futures.ProcessPoolExecutor(max_workers=num_workers) as executor:
        for i in range(num_workers):
            executor.submit(diagonal_partition_worker(input_q, output_q, chunk_size, i))


def diagonal_partition_worker(input_q: queue.Queue[str], output_q: queue.Queue[str], chunk_size: int, instance: int) -> None:
    while True:
        line = input_q.get()
        if line == SENTINEL_VALUE:
            input_q.task_done()
            break

        run_args = ["python", "/jetstream2/scratch/rico/job-dir/tool_files/diagonal_partition.py", str(chunk_size)]
        for word in line.split():
            run_args.append(word)
        process = subprocess.run(run_args, stdin=subprocess.DEVNULL, stdout=subprocess.PIPE, stderr=subprocess.PIPE, text=True)

        for line in process.stdout.splitlines():

    if not skip_segalign:
        run_args = ["segalign"]
        run_args.extend(segalign_args)
        run_args.append("--num_threads")
        run_args.append(str(args.num_cpu))

        if args.debug:
            beg: int = time.monotonic_ns()
            r_beg = resource.getrusage(resource.RUSAGE_CHILDREN)

9:08e987868f0f

    if args.debug:
        print(f"estimated chunk size: {chunk_size}", file=sys.stderr, flush=True)

    with concurrent.futures.ProcessPoolExecutor(max_workers=num_workers) as executor:
        for i in range(num_workers):
            executor.submit(diagonal_partition_worker(args, input_q, output_q, chunk_size, i))


def diagonal_partition_worker(args: argparse.Namespace, input_q: queue.Queue[str], output_q: queue.Queue[str], chunk_size: int, instance: int) -> None:
    while True:
        line = input_q.get()
        if line == SENTINEL_VALUE:
            input_q.task_done()
            break

        run_args = ["python", f"{args.tool_directory}/diagonal_partition.py", str(chunk_size)]
        for word in line.split():
            run_args.append(word)
        process = subprocess.run(run_args, stdin=subprocess.DEVNULL, stdout=subprocess.PIPE, stderr=subprocess.PIPE, text=True)

        for line in process.stdout.splitlines():

    if not skip_segalign:
        run_args = ["segalign"]
        run_args.extend(segalign_args)
        run_args.append("--num_threads")
        run_args.append(str(args.num_cpu))
        run_args.append("work/")

        if args.debug:
            beg: int = time.monotonic_ns()
            r_beg = resource.getrusage(resource.RUSAGE_CHILDREN)