[Errno 2] No such file or directory, when running galaxy in local

gbbio · November 24, 2021, 10:04am

which version of galaxy are you using and are you by any coincidence uploading a xlsx file?

xlsx format is not recognize

opened 10:15AM - 16 Jul 19 UTC

closed 01:32PM - 20 Aug 19 UTC

on galaxy 19_05 we can't upload an xlsx file and let galaxy sniff the datatype. … it works when you set the datatype yourself. the errors on galaxy.eu and galaxy.org are different... I have the same error as galaxy.org on my instance. galaxy.eu > Fatal error: Exit code 1 () > [Errno 2] No such file or directory: SafeStringWrapper(unicode:__lt__class __sq__galaxy.tools.wrappers.ToolParameterValueWrapper__sq____gt__,__lt__class __sq__galaxy.util.object_wrapper.SafeStringWrapper__sq____gt__,__lt__class __sq__numbers.Number__sq___ galaxy.org: > Traceback (most recent call last): > File "/cvmfs/main.galaxyproject.org/galaxy/tools/data_source/upload.py", line 326, in <module> > __main__() > File "/cvmfs/main.galaxyproject.org/galaxy/tools/data_source/upload.py", line 319, in __main__ > metadata.append(add_file(dataset, registry, output_path)) > File "/cvmfs/main.galaxyproject.org/galaxy/tools/data_source/upload.py", line 128, in add_file > convert_spaces_to_tabs=dataset.space_to_tab, > File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/upload_util.py", line 54, in handle_upload > convert_spaces_to_tabs=convert_spaces_to_tabs, > File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/sniff.py", line 724, in handle_uploaded_dataset_file_internal > auto_decompress=auto_decompress, > File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/sniff.py", line 663, in handle_compressed_file > sniffed_ext = run_sniffers_raw(filename, sniff_datatypes) > File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/sniff.py", line 482, in run_sniffers_raw > file_prefix = FilePrefix(filename_or_file_prefix) > File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/sniff.py", line 541, in __init__ > compressed_format, f = compression_utils.get_fileobj_raw(filename, "rb") > File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/util/compression_utils.py", line 50, in get_fileobj_raw > with zipfile.ZipFile(filename, mode) as zh: > File "/cvmfs/main.galaxyproject.org/python/lib/python2.7/zipfile.py", line 729, in __init__ > raise RuntimeError('ZipFile() requires mode "r", "w", or "a"') > RuntimeError: ZipFile() requires mode "r", "w", or "a"

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[Errno 2] No such file or directory, when running galaxy in local

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