install oligotyping error

[Courtney Swink]

Hello,

I have followed your very useful installation guide and everything worked fine up until I tried "sudo pip install oligotyping" and received the following error message:

Collecting oligotyping

  Downloading https://files.pythonhosted.org/packages/70/5a/1668b4de5108da84cb7ba3d5ec185d908608fa4c6dcfb9f2db17eac35411/oligotyping-2.1.tar.gz (2.6MB)

     |████████████████████████████████| 2.6MB 1.5MB/s 

    ERROR: Command errored out with exit status 1:

     command: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/tmp/pip-install-iJeMMM/oligotyping/setup.py'"'"'; __file__='"'"'/private/tmp/pip-install-iJeMMM/oligotyping/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base pip-egg-info

         cwd: /private/tmp/pip-install-iJeMMM/oligotyping/

    Complete output (5 lines):

    Traceback (most recent call last):

      File "<string>", line 1, in <module>

      File "/private/tmp/pip-install-iJeMMM/oligotyping/setup.py", line 5, in <module>

        from pip.req import parse_requirements

    ImportError: No module named req

    ----------------------------------------

ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.

echo $PATH

/opt/local/bin:/opt/local/sbin:/Library/Frameworks/Python.framework/Versions/2.7/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/ncbi/blast/bin

which python

/opt/local/bin/python

pip --version

pip 19.2.1 from /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pip (python 2.7)

Running on macOS Mojave version 10.14.5

Any others experience this error? I'm new to coding in terminal.

Thanks!!

Courtney 

[A. Murat Eren]

Hi Courtney, 

Apologies for the stale state of the codebase. It has been more than 5 years since I shifted my focus towards 'omics and have not improved the oligotyping codebase. If you downgrade your pip version it will work (python -m pip install pip==9.0.3), but it is best if you do it in a virtual Python environment. If you are not comfortable with these terms, I would suggest you to ask help from your local computer gurus.

Best wishes,

--

A. Murat Eren (Meren)
http://merenlab.org :: twitter :: gpg

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[Hans Schrieke]

Hi,

I had the same error I have downgraded pip in version 9.0.3 to install oligotyping. It works :

  Collecting oligotyping
  Downloading https://files.pythonhosted.org/packages/70/5a/1668b4de5108da84cb7ba3d5ec185d908608fa4c6dcfb9f2db17eac35411/oligotyping-2.1.tar.gz (2.6MB)

    100% |████████████████████████████████| 2.6MB 218kB/s
Requirement already satisfied: Matplotlib in /usr/lib/python3/dist-packages (from oligotyping)
Requirement already satisfied: BioPython in /usr/local/lib/python3.5/dist-packages (from oligotyping)
Requirement already satisfied: SciPy in /usr/local/lib/python3.5/dist-packages (from oligotyping)
Requirement already satisfied: Django in /usr/lib/python3/dist-packages (from oligotyping)
Requirement already satisfied: numpy in /usr/local/lib/python3.5/dist-packages (from BioPython->oligotyping)
Installing collected packages: oligotyping
  Running setup.py install for oligotyping ... done
Successfully installed oligotyping-2.1

But when I run the command oligotype --help , I have this error :

  File "/usr/local/bin/oligotype", line 25
    ''' % (os.path.realpath(os.path.abspath(os.path.split(inspect.getfile(inspect.currentframe()))[0])))
      ^
SyntaxError: invalid syntax

What can I do to correct it ?

Thanks!

Best wishes,

Hans

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[Courtney Swink]

Thanks so much, that fixed my problem!

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