Mercurial > repos > charles-bernard > alfa
changeset 26:f1a20d50c495 draft
Uploaded
| author | charles-bernard |
|---|---|
| date | Mon, 31 Oct 2016 14:06:36 -0400 |
| parents | 37fce32b0298 |
| children | c3f91012ac19 |
| files | ALFA/ALFA_wrapper.py |
| diffstat | 1 files changed, 1 insertions(+), 11 deletions(-) [+] |
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--- a/ALFA/ALFA_wrapper.py Mon Oct 31 14:06:18 2016 -0400 +++ b/ALFA/ALFA_wrapper.py Mon Oct 31 14:06:36 2016 -0400 @@ -40,19 +40,10 @@ parser.add_argument('--threshold', dest='threshold', action='store', nargs=2, metavar=('yMin', 'yMax'), type=float) #Internal variables parser.add_argument('--log_report', dest='log_report', action='store', nargs=1, metavar='log_filename', type=str) - parser.add_argument('--galaxy_root', dest='GALAXY_ROOT_DIR', action='store', nargs=1, metavar='galaxy_root_path', type=str) parser.add_argument('--tool_dir', dest='GALAXY_TOOL_DIR', action='store', nargs=1, metavar='galaxy_tool_dir_path', type=str) args = parser.parse_args() return args -def make_tmp_dir(galaxy_root): - parent_dir = os.path.join(galaxy_root, 'database/tmp/') - if os.path.exists(parent_dir): - tmp_dir = tempfile.mkdtemp(prefix='tmp', suffix='', dir=parent_dir) - else: - tmp_dir = tempfile.mkdtemp(prefix='tmp', suffix='', dir='.') - return tmp_dir - def mv_and_rename_user_indexes(stranded_index, unstranded_index): index='index' shutil.copy(stranded_index, index + '.stranded.index') @@ -109,8 +100,7 @@ if not (args.output_pdf or args.output_png or args.output_svg or args.output_indexes or args.output_count): exit_and_explain('Error: no output to return\nProcess Aborted\n') - tmp_dir = make_tmp_dir(args.GALAXY_TOOL_DIR[0]) - os.chdir(tmp_dir) + tmp_dir = tempfile.mkdtemp(prefix='tmp', suffix='') logging.basicConfig(level=logging.INFO, filename=args.log_report[0], filemode="a+", format='%(message)s')