run_resfinder.py Dockerfile test error
hi ,verythanks resfinder.
because of apt source ,I modyfied dockerfile with baseimages from ‘FROM debian:stretch' to 'FROM ubuntu:18.04’,and it finally build success.
when run testfiles with docker follow the tutories,it return me a error message:
\$ docker run --rm -it -v $(pwd)/db_resfinder/:/usr/src/db_resfinder -v $(pwd)/results/:/usr/src/results resfinder -ifa /usr/src/tests/data/test_isolate_01.fa -acq -db_res /usr/src/db_resfinder -o /usr/src/results
Traceback (most recent call last):
File "/usr/src/run_resfinder.py", line 338, in <module>
args.db_path_res)
File "/usr/src/cge/standardize_results.py", line 288, in load_database_metadata
version, commit = Generator.get_version_commit(db_dir)
File "/usr/src/cge/out/util/generator.py", line 38, in get_version_commit
com2tag[tag.commit.hexsha] = str(tag)
File "/usr/local/lib/python3.6/dist-packages/git/refs/tag.py", line 29, in commit
obj = self.object
File "/usr/local/lib/python3.6/dist-packages/git/refs/symbolic.py", line 190, in _get_object
return Object.new_from_sha(self.repo, hex_to_bin(self.dereference_recursive(self.repo, self.path)))
File "/usr/local/lib/python3.6/dist-packages/git/objects/base.py", line 83, in new_from_sha
oinfo = repo.odb.info(sha1)
File "/usr/local/lib/python3.6/dist-packages/git/db.py", line 43, in info
hexsha, typename, size = self._git.get_object_header(bin_to_hex(binsha))
File "/usr/local/lib/python3.6/dist-packages/git/cmd.py", line 1189, in get_object_header
return self.__get_object_header(cmd, ref)
File "/usr/local/lib/python3.6/dist-packages/git/cmd.py", line 1178, in __get_object_header
return self._parse_object_header(cmd.stdout.readline())
File "/usr/local/lib/python3.6/dist-packages/git/cmd.py", line 1138, in _parse_object_header
raise ValueError("SHA could not be resolved, git returned: %r" % (header_line.strip()))
ValueError: SHA could not be resolved, git returned: b''
Comments (2)
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Hello,
Thank you for your message and for using ResFinder.
I was not able to reproduce your error with either FROM debian:stretch' or 'FROM ubuntu:18.04’
I did find someone having similar issues which suggest to update git, see link for the full discussion: https://github.com/gitpython-developers/GitPython/issues/1016
They also suggest that the issue might be that git is running into a different owner than the repository.
Inside repo, you can try this command:
git config --global -add safe.directory <repo_path>
I hope this helps.
Best regards Maja, CGE Helpdesk