Snakefile

import os
from contextlib import contextmanager
from time import sleep, time

@contextmanager
def Lockfile(path, timeout = 5 * 60):
    started = time()

    while (time() - started) < timeout:
        try:
            lock = os.open(path, os.O_RDONLY | os.O_CREAT | os.O_EXCL)
        except FileExistsError:
            # didn't get the lock; try again in 0.1s.
            sleep(0.1)
        else:
            break
    else:
        raise TimeoutError(f"couldn't acquire lock within {timeout}s")

    try:
        yield
    finally:
        os.close(lock)
        os.unlink(path)


rule deploy:
    input: expand("{x}.deploy", x=list("abcd"))

rule deploy_one:
    output: "{x}.deploy"
    run:
        with Lockfile("deploy.lock"):
            shell("""
                sleep 2
                touch {output:q}
            """)