Resolve "Logs are not kept when a file with the same name as the logs folder name exists"

Here is what I did to test this bugfix/feature:

$ touch logs
$ bin/jman submit -- python
Traceback (most recent call last):
  File "bin/jman", line 23, in <module>
    sys.exit(gridtk.script.jman.main())
  File "gridtk/gridtk/script/jman.py", line 383, in main
    args.func(args)
  File "gridtk/gridtk/script/jman.py", line 137, in submit
    job_id = jm.submit(args.job, **kwargs)
  File "gridtk/gridtk/sge.py", line 102, in submit
    job_id = self._submit_to_grid(job, name, array, dependencies, log_dir, verbosity, **kwargs)
  File "gridtk/gridtk/sge.py", line 63, in _submit_to_grid
    assert os.path.isdir(job.log_dir), 'Please make sure --log-dir either does not exist or is a directory.'
AssertionError: Please make sure --log-dir `logs' either does not exist or is a directory.