def __init__(self, func):
Task.__init__(self, func)
self.modules = ['bioinfo-tools']
self.cmd = []
# If this is first task initialize an class holder for the session
if Drmtask.drm is None:
Drmtask.drm = drmaa.Session()
Drmtask.drm.initialize()
self.jt = self.drm.createJobTemplate()
def __init__(self, func):
Task.__init__(self, func)
self.sbatch_command = "sbatch"
self.sbatch_opts = dict((x,y) for x,y in zip(self._sbatch_kw, self._sbatch_vals))
self.sbatch_opts['A'] = self.project_name
self.sbatch_opts['D'] = self.sample_dir / str(self.sample)
self.sbatch_opts['J'] = self.__name__ + "." + str(self.sample)
self.sbatch_opts['e'] = self.__name__ + ".stderr"
self.sbatch_opts['o'] = self.__name__ + ".stdout"
self.modules = ['bioinfo-tools']