def __init__(self,
snakefile=None,
snakemakepath=None,
jobscript=None,
overwrite_shellcmd=None,
overwrite_config=dict(),
overwrite_workdir=None,
overwrite_configfile=None,
overwrite_clusterconfig=dict(),
config_args=None,
debug=False):
"""
Create the controller.
"""
self._rules = OrderedDict()
self.first_rule = None
self._workdir = None
self.overwrite_workdir = overwrite_workdir
self.workdir_init = os.path.abspath(os.curdir)
self._ruleorder = Ruleorder()
self._localrules = set()
self.linemaps = dict()
self.rule_count = 0
self.basedir = os.path.dirname(snakefile)
self.snakefile = os.path.abspath(snakefile)
self.snakemakepath = snakemakepath
self.included = []
self.included_stack = []
self.jobscript = jobscript
self.persistence = None
self.global_resources = None
self.globals = globals()
self._subworkflows = dict()
self.overwrite_shellcmd = overwrite_shellcmd
self.overwrite_config = overwrite_config
self.overwrite_configfile = overwrite_configfile
self.overwrite_clusterconfig = overwrite_clusterconfig
self.config_args = config_args
self._onsuccess = lambda log: None
self._onerror = lambda log: None
self._onstart = lambda log: None
self._wildcard_constraints = dict()
self.debug = debug
self._rulecount = 0
global config
config = dict()
config.update(self.overwrite_config)
global cluster_config
cluster_config = dict()
cluster_config.update(self.overwrite_clusterconfig)
global rules
rules = Rules()
def __init__(self, snakefile=None, snakemakepath=None, jobscript=None):
"""
Create the controller.
"""
self._rules = OrderedDict()
self.first_rule = None
self._workdir = None
self._ruleorder = Ruleorder()
self._localrules = set()
self.linemaps = dict()
self.rule_count = 0
self.basedir = os.path.dirname(snakefile)
self.snakefile = os.path.abspath(snakefile)
self.snakemakepath = os.path.abspath(snakemakepath)
self.jobscript = jobscript
self.persistence = None
self.global_resources = None
self.globals = globals()
self._subworkflows = dict()
def __init__(
self,
snakefile=None,
jobscript=None,
overwrite_shellcmd=None,
overwrite_config=dict(),
overwrite_workdir=None,
overwrite_configfiles=None,
overwrite_clusterconfig=dict(),
overwrite_threads=dict(),
config_args=None,
debug=False,
verbose=False,
use_conda=False,
conda_prefix=None,
use_singularity=False,
use_env_modules=False,
singularity_prefix=None,
singularity_args="",
shadow_prefix=None,
mode=Mode.default,
wrapper_prefix=None,
printshellcmds=False,
restart_times=None,
attempt=1,
default_remote_provider=None,
default_remote_prefix="",
run_local=True,
default_resources=None,
cache=None,
nodes=1,
cores=1,
resources=None,
conda_cleanup_pkgs=False,
):
"""
Create the controller.
"""
self.global_resources = dict() if resources is None else resources
self.global_resources["_cores"] = cores
self.global_resources["_nodes"] = nodes
self._rules = OrderedDict()
self.first_rule = None
self._workdir = None
self.overwrite_workdir = overwrite_workdir
self.workdir_init = os.path.abspath(os.curdir)
self._ruleorder = Ruleorder()
self._localrules = set()
self.linemaps = dict()
self.rule_count = 0
self.basedir = os.path.dirname(snakefile)
self.snakefile = os.path.abspath(snakefile)
self.included = []
self.included_stack = []
self.jobscript = jobscript
self.persistence = None
self.globals = globals()
self._subworkflows = dict()
self.overwrite_shellcmd = overwrite_shellcmd
self.overwrite_config = overwrite_config
self.overwrite_configfiles = overwrite_configfiles
self.overwrite_clusterconfig = overwrite_clusterconfig
self.overwrite_threads = overwrite_threads
self.config_args = config_args
self.immediate_submit = None
self._onsuccess = lambda log: None
self._onerror = lambda log: None
self._onstart = lambda log: None
self._wildcard_constraints = dict()
self.debug = debug
self.verbose = verbose
self._rulecount = 0
self.use_conda = use_conda
self.conda_prefix = conda_prefix
self.use_singularity = use_singularity
self.use_env_modules = use_env_modules
self.singularity_prefix = singularity_prefix
self.singularity_args = singularity_args
self.shadow_prefix = shadow_prefix
self.global_container_img = None
self.mode = mode
self.wrapper_prefix = wrapper_prefix
self.printshellcmds = printshellcmds
self.restart_times = restart_times
self.attempt = attempt
self.default_remote_provider = default_remote_provider
self.default_remote_prefix = default_remote_prefix
self.configfiles = []
self.run_local = run_local
self.report_text = None
self.conda_cleanup_pkgs = conda_cleanup_pkgs
# environment variables to pass to jobs
# These are defined via the "envvars:" syntax in the Snakefile itself
self.envvars = set()
self.enable_cache = False
if cache is not None:
self.enable_cache = True
self.cache_rules = set(cache)
if self.default_remote_provider is not None:
self.output_file_cache = RemoteOutputFileCache(
self.default_remote_provider)
else:
self.output_file_cache = LocalOutputFileCache()
else:
self.output_file_cache = None
self.cache_rules = set()
if default_resources is not None:
self.default_resources = default_resources
else:
# only _cores and _nodes
self.default_resources = DefaultResources()
self.iocache = snakemake.io.IOCache()
global config
config = copy.deepcopy(self.overwrite_config)
global cluster_config
cluster_config = copy.deepcopy(self.overwrite_clusterconfig)
global rules
rules = Rules()
global checkpoints
checkpoints = Checkpoints()
def __init__(self,
snakefile=None,
jobscript=None,
overwrite_shellcmd=None,
overwrite_config=dict(),
overwrite_workdir=None,
overwrite_configfile=None,
overwrite_clusterconfig=dict(),
config_args=None,
debug=False,
use_conda=False,
conda_prefix=None,
use_singularity=False,
singularity_prefix=None,
singularity_args="",
use_docker=False,
docker_args="",
shadow_prefix=None,
mode=Mode.default,
wrapper_prefix=None,
printshellcmds=False,
restart_times=None,
attempt=1,
default_remote_provider=None,
default_remote_prefix="",
run_local=True,
default_resources=dict()):
"""
Create the controller.
"""
self._rules = OrderedDict()
self.first_rule = None
self._workdir = None
self.overwrite_workdir = overwrite_workdir
self.workdir_init = os.path.abspath(os.curdir)
self._ruleorder = Ruleorder()
self._localrules = set()
self.linemaps = dict()
self.rule_count = 0
self.basedir = os.path.dirname(snakefile)
self.snakefile = os.path.abspath(snakefile)
self.included = []
self.included_stack = []
self.jobscript = jobscript
self.persistence = None
self.global_resources = None
self.globals = globals()
self._subworkflows = dict()
self.overwrite_shellcmd = overwrite_shellcmd
self.overwrite_config = overwrite_config
self.overwrite_configfile = overwrite_configfile
self.overwrite_clusterconfig = overwrite_clusterconfig
self.config_args = config_args
self.immediate_submit = None
self._onsuccess = lambda log: None
self._onerror = lambda log: None
self._onstart = lambda log: None
self._wildcard_constraints = dict()
self.debug = debug
self._rulecount = 0
self.use_conda = use_conda
self.conda_prefix = conda_prefix
self.use_singularity = use_singularity
self.singularity_prefix = singularity_prefix
self.singularity_args = singularity_args
self.use_docker = use_docker
self.docker_args = docker_args
self.shadow_prefix = shadow_prefix
self.global_singularity_img = None
self.mode = mode
self.wrapper_prefix = wrapper_prefix
self.printshellcmds = printshellcmds
self.restart_times = restart_times
self.attempt = attempt
self.default_remote_provider = default_remote_provider
self.default_remote_prefix = default_remote_prefix
self.configfiles = []
self.run_local = run_local
self.report_text = None
self.default_resources = dict(_cores=1, _nodes=1)
self.default_resources.update(default_resources)
self.iocache = snakemake.io.IOCache()
global config
config = copy.deepcopy(self.overwrite_config)
global cluster_config
cluster_config = copy.deepcopy(self.overwrite_clusterconfig)
global rules
rules = Rules()
global checkpoints
checkpoints = Checkpoints()
