c8952cd00253c2c8176b7d2e3bf39bf93c639b72,atlas/rules/initialize_checkm.py,,,#,56

Before Change

    stdout = p.communicate(input=newline.join(response) if isinstance(response, list) else response)[0]


with open(snakemake.log[0],"w") as errlog:

    run_popen(["checkm", "data", "setRoot"], [snakemake.params.database_dir, snakemake.params.database_dir],errlog)
    run_popen(["checkm", "data", "update"], ["y", "y"],errlog)

// when re-activating a conda env, reset the .dmanifest directory and download
with open(snakemake.output.touched_output, "w") as fh:
    fh.write("CheckM successfully initialized.\n")

After Change

        fh.write("CheckM successfully initialized.\n")


if __name__ == "__main__":
    p = argparse.ArgumentParser(description=__doc__,
            formatter_class=argparse.ArgumentDefaultsHelpFormatter)

    p.add_argument("dbdir", help="path to database directory")
    p.add_argument("confirmation", help="path to touched file confirming completion")
    p.add_argument("log", help="stderr output of checkm setup")
    args = p.parse_args()
    logging.basicConfig(level=logging.INFO, datefmt="%Y-%m-%d %H:%M",
        format="[%(asctime)s] %(message)s")
    main(args.dbdir, args.confirmation, args.log)

Instances