Galaxy tool is giving errror

[JayanthiGangiredla]

Thanks you for developing a galaxy wrapper on this tool. However, the tool is giving error while trying to downooad cgmlst database. Please help fixing it. We use this tool a lot in our research..

[INFO: 2025-06-18 14:29:22,429] One element found : Pseudomonas aeruginosa
[INFO: 2025-06-18 14:29:22,430] Downloading the core genome...
Traceback (most recent call last):
File "/usr/local/bin/wgMLST", line 10, in
sys.exit(wg())
^^^^
File "/usr/local/lib/python3.11/site-packages/click/core.py", line 1157, in call
return self.main(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/pymlst/wg/commands/import.py", line 52, in cli
skipped = web.get_cgmlst_file(url, tmp)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/pymlst/common/web.py", line 218, in get_cgmlst_file
with tempfile.TemporaryDirectory() as tmp_dir:
File "/usr/local/lib/python3.11/tempfile.py", line 904, in exit
self.cleanup()
File "/usr/local/lib/python3.11/tempfile.py", line 908, in cleanup
self._rmtree(self.name, ignore_errors=self._ignore_cleanup_errors)
File "/usr/local/lib/python3.11/tempfile.py", line 890, in _rmtree
_shutil.rmtree(name, onerror=onerror)
File "/usr/local/lib/python3.11/shutil.py", line 731, in rmtree
_rmtree_safe_fd(fd, path, onerror)
File "/usr/local/lib/python3.11/shutil.py", line 665, in _rmtree_safe_fd
onerror(os.rmdir, fullname, sys.exc_info())
File "/usr/local/lib/python3.11/shutil.py", line 663, in _rmtree_safe_fd
os.rmdir(entry.name, dir_fd=topfd)
OSError: [Errno 39] Directory not empty: 'fas'

[bvalot]

Hi,

Can you give me more informations of which versions of pymlst and galaxy wrapper is use?
This is a public or private galaxy instance?

benoit

[JayanthiGangiredla]

I used both 2.1.5+galaxy0. and. 2.1.3+galaxy1 on galaxy version24

[JayanthiGangiredla]

This is a private galaxy for FDA research.

[bvalot]

What is the version of pymlst install with conda?

[bvalot]

This seems to be an problem of delete temporary dir.
Never seen this error and my current galaxy installation ( Galaxy Version 2.1.3+galaxy1) with the same wrapper works fine.

[JayanthiGangiredla]

Ok.Thanks for letting me know. We have our previous galaxy software version 21 and currently we are upgrading to Galaxy 24. The tool was working fine in 21 version of galaxy. I think is an error related to singularity containers. I will check at our end. Thank you!

[bvalot]

OK, I see. I would make test with this information to reproduce bug.

[bvalot]

I make test with planemo on 24.2, but found not error.
Do you have always problem in your galaxy instance?

[JayanthiGangiredla]

thank you. Let me check at our end. Thank you for your time!

-Jayanthi