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Installation issue on CentOS

See original GitHub issue

Hi, I’m attempting to install this on CentOS but running into the attached error - any thoughts?

Cheers Oli

user@c112384:~/software/OmegaFold$ pip install -r requirements.txt
Exception:
Traceback (most recent call last):
  File "/usr/lib/python2.7/site-packages/pip/basecommand.py", line 215, in main
    status = self.run(options, args)
  File "/usr/lib/python2.7/site-packages/pip/commands/install.py", line 257, in run
    with self._build_session(options) as session:
  File "/usr/lib/python2.7/site-packages/pip/basecommand.py", line 69, in _build_session
    if options.cache_dir else None
  File "/usr/lib64/python2.7/posixpath.py", line 77, in join
    elif path == '' or path.endswith('/'):
AttributeError: 'int' object has no attribute 'endswith'
Traceback (most recent call last):
  File "/usr/bin/pip", line 9, in <module>
    load_entry_point('pip==8.1.2', 'console_scripts', 'pip')()
  File "/usr/lib/python2.7/site-packages/pip/__init__.py", line 220, in main
    return command.main(cmd_args)
  File "/usr/lib/python2.7/site-packages/pip/basecommand.py", line 251, in main
    timeout=min(5, options.timeout)) as session:
  File "/usr/lib/python2.7/site-packages/pip/basecommand.py", line 69, in _build_session
    if options.cache_dir else None
  File "/usr/lib64/python2.7/posixpath.py", line 77, in join
    elif path == '' or path.endswith('/'):
AttributeError: 'int' object has no attribute 'endswith'

Issue Analytics

  • State:closed
  • Created a year ago
  • Comments:5 (2 by maintainers)

github_iconTop GitHub Comments

1reaction
RuiWang1998commented, Aug 9, 2022

Just try the old way, use python main.py INPUT_FILE.fasta OUTPUT_DIRECTORY, the omegafold INPUT_FILE.fasta OUTPUT_DIRECTORY only works if you python setup.py install first or use the pip install git+ command, sorry for the confusion, we are going to update that ASAP.

1reaction
olibclarkecommented, Aug 9, 2022

Thanks Rui - I have python 3 available on the system, but 2.75 is the default system python. Now that I realize the cause of the error, running as python3.8 -m pip install -r requirements.txt allows installation to proceed successfully. Thanks!

Read more comments on GitHub >

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