plasmid_atlas

#!/usr/bin/env python3

import os,sys
path= os.path.dirname(__file__)

from snakemake.shell import shell

atlas_folder=sys.argv[1]
database_dir=sys.argv[2]
snakemake_args= sys.argv[3:]

shell(
    "snakemake --config database_dir={database_dir} "
    " -s {path}/Snakefile "
    "-d {atlas_folder} "
    "--use-conda --conda-prefix {database_dir}/conda_envs/ "
    "{snakemake_args}"
    )