Retrieve Galaxy *.loc file for the given reference/aligner name.

    First tries to find an aligner specific *.loc file. If not defined
    or does not exist, then we need to try and remap it from the
    default reference file

def _get_galaxy_loc_file(name, galaxy_dt, ref_dir, galaxy_base):
    """Retrieve Galaxy *.loc file for the given reference/aligner name.

    First tries to find an aligner specific *.loc file. If not defined
    or does not exist, then we need to try and remap it from the
    default reference file
    """
    if "file" in galaxy_dt and os.path.exists(os.path.join(galaxy_base, galaxy_dt["file"])):
        loc_file = os.path.join(galaxy_base, galaxy_dt["file"])
        need_remap = False
    elif alignment.TOOLS[name].galaxy_loc_file is None:
        loc_file = os.path.join(ref_dir, alignment.BASE_LOCATION_FILE)
        need_remap = True
    else:
        loc_file = os.path.join(ref_dir, alignment.TOOLS[name].galaxy_loc_file)
        need_remap = False
    if not os.path.exists(loc_file):
        loc_file = os.path.join(ref_dir, alignment.BASE_LOCATION_FILE)
        need_remap = True
    return loc_file, need_remap