utils.snk

import os
import shutil

ROOTPATH = os.path.dirname(os.path.dirname(workflow.snakefile))
sys.path.insert(0, os.path.join(ROOTPATH, "lib"))
os.environ["PYTHONPATH"] = os.path.join(ROOTPATH, "lib")


def get_threads(rule, default):
    cluster_config = snakemake.workflow.cluster_config
    if rule in cluster_config and "threads" in cluster_config[rule]:
        return cluster_config[rule]["threads"]
    if "default" in cluster_config and "threads" in cluster_config["default"]:
        return cluster_config["default"]["threads"]
    return default


def get_perl5lib():
    condaprefix = os.environ["CONDA_PREFIX"]
    perllibpath = os.path.join(condaprefix, "lib", "perl5")
    return perllibpath