run_singularity.py doesn't use output_dir flag

[mokca]

The run_singularity.py script has an --output_dir flag but doesn't appear to use it.

The flags summary says

  --output_dir: Path to a directory that will store the results.
    (default: '/tmp')

However, output_dir is set to the contents of TMP or TMPDIR if defined, or a generated temporary directory in tmp.

if 'TMP' in os.environ:
    output_dir = os.environ['TMP']
elif 'TMPDIR' in os.environ:
    output_dir = os.environ['TMPDIR']
else:
    output_dir = tempfile.mkdtemp(dir='/tmp', prefix='alphafold-')

The contents of FLAGS.output_dir don't appear to be used at any stage.

[prehensilecode]

The variable tmp_dir is set to the value of output_dir. Then, tmp_dir is used for the bind in line 237.

[prehensilecode]

Duplicate of #31