OBITools installation error (mac OS X)

Question

[mariahaguiar001]

Hi everyone, I am attempting to install OBITools and I receive the following error:

$ pip3 install OBITools
    Collecting OBITools
     Using cached    https://files.pythonhosted.org/packages/dc/53/bef677cfebef9aba707abb36f476d474c1a3d67f02fefdb38fa9fcf92b4f/OBITools-1.2.11.tar.gz
    Complete output from command python setup.py egg_info:
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/private/var/folders/bv/3wwlmnhs7vz0k9ffnhcx674c0000gn/T/pip-build-skycz3ut/OBITools/setup.py", line 35, in <module>
        from obidistutils.serenity import serenity_mode
      File "distutils.ext/obidistutils/serenity/__init__.py", line 12, in <module>
        import urllib2
    ModuleNotFoundError: No module named 'urllib2'

    ----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /private/var/folders/bv/3wwlmnhs7vz0k9ffnhcx674c0000gn/T/pip-build-skycz3ut/OBITools/

If anyone could point me in the right direction that would be great, thanks for reading!

[Devon Ryan]

It appears OBITools is for python 2 only. So pip2 install it.

[mariahaguiar001]

Yes, I tried pip and pip2 to install OBITools but it reports that the command is not found.

[GenoMax]

What command is not found?

[mariahaguiar001]

pip2 does not work. I installed pip, it seemed to work, however, I received the same error message as before.

[GenoMax]

Can you post the output of which -a python and which -a python3?

[mariahaguiar001]

$which -a python
/usr/bin/python


$ which -a python3
/Library/Frameworks/Python.framework/Versions/3.6/bin/python3
/usr/local/bin/python3

[WouterDeCoster]

I installed pip

How? Can you show which -a pip?

What about

python -m pip install OBITools

[mariahaguiar001]

$ which -a pip
/Library/Frameworks/Python.framework/Versions/3.6/bin/pip

I also tried python -m pip install OBITools, and it returned /usr/bin/python: No module named pip

[WouterDeCoster]

Then pip was not installed for python2

[GenoMax]

I installed pip, it seemed to work, however, I received the same error message as before.

The reason you are getting the same error is because pip you are using is for python3.

[Roman Luštrik]

If you're not against dockers, I've made a dockerized version of the tool, which abstracts away the arduous install process. https://hub.docker.com/r/romunov/obitools