# A simple CLI runner for slurm that can be used when running Galaxy from a
# non-submit host and using a Slurm cluster.
from ..job import BaseJobExec
from logging import getLogger
try:
from galaxy.model import Job
job_states = Job.states
except ImportError:
# Not in Galaxy, map Galaxy job states to Pulsar ones.
from pulsar.util import enum
job_states = enum(RUNNING='running', OK='complete', QUEUED='queued', ERROR="failed")
log = getLogger(__name__)
argmap = {
'time': '-t',
'ncpus': '-c',
'partition': '-p'
}
class Slurm(BaseJobExec):
def __init__(self, **params):
self.params = {}
for k, v in params.items():
self.params[k] = v
from logging import getLogger
try:
from galaxy.model import Job
job_states = Job.states
except ImportError:
# Not in Galaxy, map Galaxy job states to Pulsar ones.
from pulsar.util import enum
job_states = enum(RUNNING='running', OK='complete', QUEUED='queued')
from galaxy.util import parse_xml_string
from ..job import BaseJobExec
log = getLogger(__name__)
ERROR_MESSAGE_UNRECOGNIZED_ARG = 'Unrecognized long argument passed to Torque CLI plugin: %s'
argmap = {
'destination': '-q',
'Execution_Time': '-a',
'Account_Name': '-A',
'Checkpoint': '-c',
'Error_Path': '-e',
'Group_List': '-g',
'Hold_Types': '-h',
'Join_Paths': '-j',
'Keep_Files': '-k',
'Resource_List': '-l',
'Mail_Points': '-m',
'Mail_Users': '-M',
'Job_Name': '-N',
# A simple CLI runner for slurm that can be used when running Galaxy from a
# non-submit host and using a Slurm cluster.
from logging import getLogger
try:
from galaxy.model import Job
job_states = Job.states
except ImportError:
# Not in Galaxy, map Galaxy job states to Pulsar ones.
from pulsar.util import enum
job_states = enum(RUNNING='running',
OK='complete',
QUEUED='queued',
ERROR="failed")
from ..job import BaseJobExec
log = getLogger(__name__)
argmap = {'time': '-t', 'ncpus': '-c', 'partition': '-p'}
class Slurm(BaseJobExec):
def __init__(self, **params):
self.params = {}
for k, v in params.items():
self.params[k] = v
def job_script_kwargs(self, ofile, efile, job_name):
scriptargs = {'-o': ofile, '-e': efile, '-J': job_name}
from logging import getLogger
try:
import xml.etree.cElementTree as et
except ImportError:
import xml.etree.ElementTree as et
try:
from galaxy.model import Job
job_states = Job.states
except ImportError:
# Not in Galaxy, map Galaxy job states to Pulsar ones.
from pulsar.util import enum
job_states = enum(RUNNING='running', OK='complete', QUEUED='queued')
from ..job import BaseJobExec
log = getLogger(__name__)
ERROR_MESSAGE_UNRECOGNIZED_ARG = 'Unrecognized long argument passed to Torque CLI plugin: %s'
argmap = {'destination': '-q',
'Execution_Time': '-a',
'Account_Name': '-A',
'Checkpoint': '-c',
'Error_Path': '-e',
'Group_List': '-g',
'Hold_Types': '-h',
'Join_Paths': '-j',
'Keep_Files': '-k',
'Resource_List': '-l',
'Mail_Points': '-m',