예제 #1
0
파일: george.py 프로젝트: ewiger/gc3pie
 def __init__(self):
     SessionBasedScript.__init__(
         self,
         version = '0.3',
         # only '.txt' files are considered as valid input
         input_filename_pattern = '*.ini',
         )
예제 #2
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 def __init__(self):
     SessionBasedScript.__init__(
         self,
         version=__version__,
         application=gimc_preprocessingApplication,
         stats_only_for=gimc_preprocessingApplication,
     )
예제 #3
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 def __init__(self):
     SessionBasedScript.__init__(
         self,
         version = '0.3',
         # only '.txt' files are considered as valid input
         input_filename_pattern = '*.ini',
         )
예제 #4
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 def __init__(self):
     SessionBasedScript.__init__(
         self,
         usage="%(prog)s [options] FLAGSFILE INPUT ... [: OUTPUT ...]",
         version=__version__,  # module version == script version
         application=RosettaApplication,
     )
예제 #5
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 def __init__(self):
     SessionBasedScript.__init__(
         self,
         version=__version__,
         application=GbidsApplication,
         stats_only_for=GbidsApplication,
     )
예제 #6
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 def __init__(self):
     SessionBasedScript.__init__(
         self,
         version=__version__,  # module version == script version
         application=GParseURLApplication,
         stats_only_for=GParseURLApplication,
     )
예제 #7
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 def __init__(self):
     SessionBasedScript.__init__(
         self,
         version = __version__,
         application = Gfit3C_ABC_uml_Application,
         input_filename_pattern = '*.d',
         )
예제 #8
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 def __init__(self):
     SessionBasedScript.__init__(
         self,
         version=__version__,
         application=Gfit3C_ABC_uml_Application,
         input_filename_pattern='*.d',
     )
예제 #9
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 def __init__(self):
     SessionBasedScript.__init__(
         self,
         version=__version__,
         application=gsentitweetApplication,
         stats_only_for=gsentitweetApplication,
     )
예제 #10
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 def __init__(self):
     SessionBasedScript.__init__(
         self,
         version=__version__,  # module version == script version
         application=BidsWrappsApplication,
         stats_only_for=BidsWrappsApplication,
     )
예제 #11
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 def __init__(self):
     SessionBasedScript.__init__(
         self,
         version = __version__, # module version == script version
         application = GreductionApplication, 
         stats_only_for = GreductionApplication,
         )
예제 #12
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 def __init__(self):
     SessionBasedScript.__init__(
         self,
         version = __version__,
         application = GpartialequilibriumApplication, 
         stats_only_for = GpartialequilibriumApplication,
         )
예제 #13
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 def __init__(self):
     SessionBasedScript.__init__(
         self,
         version=__version__,
         application=GpartialequilibriumApplication,
         stats_only_for=GpartialequilibriumApplication,
     )
예제 #14
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파일: gpfi.py 프로젝트: TissueMAPS/gc3pie
 def __init__(self):
     SessionBasedScript.__init__(
         self,
         version = __version__,
         application = GpfiApplication, 
         stats_only_for = GpfiApplication,
         )
예제 #15
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 def __init__(self):
     SessionBasedScript.__init__(
         self,
         version = '0.2',
         # TURBOMOLE's "coord" files are input
         input_filename_pattern = 'coord',
         )
예제 #16
0
파일: gricomp.py 프로젝트: ewiger/gc3pie
 def __init__(self):
     SessionBasedScript.__init__(
         self,
         version = '0.2',
         # TURBOMOLE's "coord" files are input
         input_filename_pattern = 'coord',
         )
예제 #17
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 def __init__(self):
     SessionBasedScript.__init__(
         self,
         version=__version__,  # module version == script version
         # application = GATKStagedTaskCollection,
         application=Application,
         stats_only_for=Application)
예제 #18
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 def __init__(self):
     SessionBasedScript.__init__(
         self,
         usage = "%(prog)s [options] FLAGSFILE INPUT ... [: OUTPUT ...]",
         version = __version__, # module version == script version
         application = RosettaApplication,
         )
예제 #19
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파일: ggatk.py 프로젝트: TissueMAPS/gc3pie
 def __init__(self):
     SessionBasedScript.__init__(
         self,
         version = __version__, # module version == script version
         # application = GATKStagedTaskCollection,
         application = Application,
         stats_only_for = Application
         )
예제 #20
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 def __init__(self):
     SessionBasedScript.__init__(
         self,
         version = '0.2',
         # only '.loop' files are considered as valid input
         input_filename_pattern = '*.loop',
     )
     forwardPremium.paraLoop_fp.__init__(self, verbosity = 'INFO')
예제 #21
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 def __init__(self):
     self.bids_app_execution = DEFAULT_DOCKER_BIDS_APP
     SessionBasedScript.__init__(
         self,
         version=__version__,
         application=GbidsApplication,
         stats_only_for=GbidsApplication,
     )
예제 #22
0
 def __init__(self):
     SessionBasedScript.__init__(
         self,
         version = '0.2',
         # only '.loop' files are considered as valid input
         input_filename_pattern = '*.loop',
     )
     paraLoop.__init__(self, 'INFO')
예제 #23
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 def __init__(self):
     SessionBasedScript.__init__(
         self,
         version='0.2',
         # only '.loop' files are considered as valid input
         input_filename_pattern='*.loop',
     )
     forwardPremium.paraLoop_fp.__init__(self, verbosity='INFO')
예제 #24
0
 def __init__(self):
     SessionBasedScript.__init__(
         self,
         version = '1.0',
         input_filename_pattern = '*.loop',
         stats_only_for = Application,
     )
     paraLoop.__init__(self, 'INFO')
예제 #25
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 def __init__(self):
     SessionBasedScript.__init__(
         self,
         version='1.0',
         input_filename_pattern='*.loop',
         stats_only_for=Application,
     )
     paraLoop.__init__(self, 'INFO')
예제 #26
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 def __init__(self):
     SessionBasedScript.__init__(
         self,
         version = '0.2',
         # only '.loop' files are considered as valid input
         input_filename_pattern = '*.loop',
     )
     paraLoop.__init__(self, 'INFO')        
예제 #27
0
파일: gmbsim.py 프로젝트: arcimboldo/gc3pie
 def __init__(self):
     SessionBasedScript.__init__(
         self,
         version = __version__, # module version == script version
         input_filename_pattern = '*.csv',
         application = GmbsimApplication,
         # only display stats for the top-level policy objects
         #stats_only_for = GmbsimApplication,
         )
예제 #28
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 def __init__(self):
     SessionBasedScript.__init__(
         self,
         version=__version__,  # module version == script version
         input_filename_pattern='*.csv',
         application=GmbsimApplication,
         # only display stats for the top-level policy objects
         #stats_only_for = GmbsimApplication,
     )
예제 #29
0
파일: gcodeml.py 프로젝트: smaffiol/gc3pie
    def __init__(self):
        SessionBasedScript.__init__(
            self,
            version = __version__, # module version == script version
            # `CodemlRetryPolicy` is the top-level object here,
            # so only print information about it.
#            stats_only_for = CodemlRetryPolicy,
             stats_only_for = gc3libs.application.codeml.CodemlApplication,
            )
예제 #30
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    def __init__(self):
        SessionBasedScript.__init__(
            self,
            version = __version__, # module version == script version
            # `CodemlRetryPolicy` is the top-level object here,
            # so only print information about it.
#            stats_only_for = CodemlRetryPolicy,
             stats_only_for = gc3libs.application.codeml.CodemlApplication,
            )
예제 #31
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 def __init__(self):
     SessionBasedScript.__init__(
         self,
         version=__version__,  # module version == script version
         # Use fully-qualified name for class,
         # to allow GC3Utils to unpickle job instances
         # see: https://github.com/uzh/gc3pie/issues/95
         application=GDockingApplication,
         input_filename_pattern='*.pdb')
예제 #32
0
 def __init__(self):
     SessionBasedScript.__init__(
         self,
         version=__version__,  # module version == script version
         # only display stats for the top-level policy objects
         # (which correspond to the processed files) omit counting
         # actual applications because their number varies over
         # time as checkpointing and re-submission takes place.
         stats_only_for=GsnowpackApplication,
     )
예제 #33
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 def __init__(self):
     SessionBasedScript.__init__(
         self,
         version = __version__, # module version == script version
         # only display stats for the top-level policy objects
         # (which correspond to the processed files) omit counting
         # actual applications because their number varies over
         # time as checkpointing and re-submission takes place.
         stats_only_for = GsnowpackApplication,
         ) 
예제 #34
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 def __init__(self):
     SessionBasedScript.__init__(
         self,
         version = __version__, # module version == script version
         application = ggamess_retry.GamessRetryPolicy,
         input_filename_pattern = '*.inp',
         # `GamessRetryPolicy` is the top-level object now,
         # so only print information about it.
         stats_only_for = ggamess_retry.GamessRetryPolicy,
         )
예제 #35
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 def __init__(self):
     SessionBasedScript.__init__(
         self,
         version = __version__, # module version == script version
         application = ggamess_retry.GamessRetryPolicy,
         input_filename_pattern = '*.inp',
         # `GamessRetryPolicy` is the top-level object now,
         # so only print information about it.
         stats_only_for = ggamess_retry.GamessRetryPolicy,
         )
예제 #36
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 def __init__(self):
     SessionBasedScript.__init__(
         self,
         version = __version__, # module version == script version
         # Use fully-qualified name for class,
         # to allow GC3Utils to unpickle job instances
         # see: https://github.com/uzh/gc3pie/issues/95
         application = GDockingApplication,
         input_filename_pattern = '*.pdb'
         )
예제 #37
0
 def __init__(self):
     SessionBasedScript.__init__(
         self,
         version="0.2",
         # only '.loop' files are considered as valid input
         input_filename_pattern="*.loop",
         stats_only_for=Application
         # idRiskApppotApplication
         # idRiskApplication,
     )
     paraLoop.__init__(self, "INFO")
예제 #38
0
 def __init__(self):
     SessionBasedScript.__init__(
         self,
         version='0.2',
         # only '.loop' files are considered as valid input
         input_filename_pattern='*.loop',
         stats_only_for=Application
         #idRiskApppotApplication
         #idRiskApplication,
     )
     paraLoop.__init__(self, 'INFO')
예제 #39
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 def __init__(self):
     SessionBasedScript.__init__(
         self,
         version=__version__,  # module version == script version
         input_filename_pattern='MHC_coev_*',
         application=GMhcCoevTask,
         # only display stats for the top-level policy objects
         # (which correspond to the processed files) omit counting
         # actual applications because their number varies over
         # time as checkpointing and re-submission takes place.
         stats_only_for=GMhcCoevTask,
     )
예제 #40
0
파일: gmhc_coev.py 프로젝트: ewiger/gc3pie
 def __init__(self):
     SessionBasedScript.__init__(
         self,
         version = __version__, # module version == script version
         input_filename_pattern = 'MHC_coev_*',
         application = GMhcCoevTask,
         # only display stats for the top-level policy objects
         # (which correspond to the processed files) omit counting
         # actual applications because their number varies over
         # time as checkpointing and re-submission takes place.
         stats_only_for = GMhcCoevTask,
         )
예제 #41
0
파일: ggeosphere.py 프로젝트: ewiger/gc3pie
 def _main_loop_exitcode(self, stats):
     """
     This works in daemon mode;
     Thus do not end if all simulations have been
     processed. Continue and wait for new models to be uploaded.
     """
     if self.extra['is_daemon']:
         return 4
     else:
         return SessionBasedScript._main_loop_exitcode(self, stats)
예제 #42
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 def _main_loop_exitcode(self, stats):
     """
     This works in daemon mode;
     Thus do not end if all simulations have been
     processed. Continue and wait for new models to be uploaded.
     """
     if self.extra['is_daemon']:
         return 4
     else:
         return SessionBasedScript._main_loop_exitcode(self, stats)
예제 #43
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    def pre_run(self):
        """
        - If instance_type or image_id are specified in the command line,
        override config file settings.
        - write session path to log path for check logs

        """
        SessionBasedScript.pre_run(self)
        if self.params.instance_type:
            self._core.resources[
                'S3ITSC'].bidswrapps_instance_type = self.params.instance_type
        if self.params.image_id:
            self._core.resources[
                'S3ITSC'].bidswrapps_image_id = self.params.image_id

        # create link to session path in output path
        out_path = self.params.output.replace("NAME", "")
        if not os.path.isdir(out_path):
            os.makedirs(out_path)
        info_file = os.path.join(out_path, ".session_path")
        with open(info_file, "w") as fi:
            fi.write(os.path.abspath(self.params.session))
예제 #44
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 def __init__(self):
     SessionBasedScript.__init__(
         self,
         version = __version__, # module version == script version
         input_filename_pattern = '*.inp'
         )
예제 #45
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 def __init__(self):
     SessionBasedScript.__init__(
         self,
         version=__version__,
     )
예제 #46
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    def process_args(self):
        from time import localtime, strftime
        # set timestamp
        self.time_stamp = strftime("%Y-%m-%d-%H%M", localtime())

        SessionBasedScript.process_args(self)
 def __init__(self):
     SessionBasedScript.__init__(
         self,
         version='0.0.1',
     )
예제 #48
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 def __init__(self):
     SessionBasedScript.__init__(self,
                                 version='0.2',
                                 stats_only_for=Application)
예제 #49
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    def process_args(self):
        from time import localtime, strftime
        # set timestamp
        self.time_stamp = strftime("%Y-%m-%d-%H%M", localtime())

        SessionBasedScript.process_args(self)
예제 #50
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 def __init__(self):
     SessionBasedScript.__init__(
         self,
         version = '0.2',
         stats_only_for = Application
     )
예제 #51
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 def __init__(self):
     SessionBasedScript.__init__(
         self,
         version='0.2',
         input_filename_pattern='*.ini',
     )
예제 #52
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 def __init__(self):
     SessionBasedScript.__init__(
         self,
         version=__version__,  # module version == script version
         application=FunctionalDiversityApplication,
     )
예제 #53
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 def __init__(self):
     SessionBasedScript.__init__(
         self,
         version = '0.3',
         # input_filename_pattern = '*.ini',
         )
예제 #54
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 def __init__(self):
     SessionBasedScript.__init__(
         self,
         version = __version__, # module version == script version
         stats_only_for = CryptoApplication,
         )
예제 #55
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파일: ghousing.py 프로젝트: ewiger/gc3pie
 def __init__(self):
     SessionBasedScript.__init__(self, version="1.0", input_filename_pattern="*.loop", stats_only_for=Application)
     paraLoop.__init__(self, "INFO")
예제 #56
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 def __init__(self):
     SessionBasedScript.__init__(
         self,
         version = __version__,
         )
예제 #57
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파일: gfdiv.py 프로젝트: fliem/gc3pie
 def __init__(self):
     SessionBasedScript.__init__(
         self,
         version = __version__, # module version == script version
         application = FunctionalDiversityApplication,
     )