koeken intall problem

I would like to installa koeken for LefSE on macqiime.

$ pip3 install https://github.com/twbattaglia/koeken/zipball/master

Collecting https://github.com/twbattaglia/koeken/zipball/master
  Downloading https://github.com/twbattaglia/koeken/zipball/master (44kB)
    100% |████████████████████████████████| 51kB 220kB/s 
    Complete output from command python setup.py egg_info:
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/private/var/folders/r0/pz5bqg7d7j7fr1dcg8slw2l80000gn/T/pip-tsggsgao-build/setup.py", line 11
        print "Attempting to install R packages...Please wait."
                                                              ^
    SyntaxError: Missing parentheses in call to 'print'. Did you mean print(print "Attempting to install R packages...Please wait.")?

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

Command "python setup.py egg_info" failed with error code 1 in /private/var/folders/r0/pz5bqg7d7j7fr1dcg8slw2l80000gn/T/pip-tsggsgao-build/

software error

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written 8.6 years ago by Giffredo •

I added markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

101010 Button

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written 8.6 years ago by WouterDeCoster

If you have MacQIIME installed, you must first initialize it before installing Koeken. If you do not have macqiime installed, you can still run koeken as long as you have the scripts available in your path.

Did you follow these instructions?

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written 8.6 years ago by h.mon

i use macqiime and I enter there before installation.

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written 8.6 years ago by Giffredo •

 MacQIIME iMac-GG:~ $ pip2 install https://github.com/twbattaglia/koeken/zipball/master

Collecting https://github.com/twbattaglia/koeken/zipball/master
  Downloading https://github.com/twbattaglia/koeken/zipball/master (44kB)
    100% |████████████████████████████████| 51kB 262kB/s 
Collecting rpy2 (from koeken==0.2.6)
  Using cached rpy2-2.9.1.tar.gz
    Complete output from command python setup.py egg_info:
    rpy2 is no longer supporting Python < 3. Consider using an older rpy2 release when using an older Python release.

    ----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /private/tmp/pip-build-LY74pm/rpy2/`enter code here`

doesn't work with python 2.7 ....

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written 8.6 years ago by Giffredo •

Would be better if you react to my post to keep the logic of this thread easy to follow.

Anyway, looks like the authors of koeken have to translate their code to py3. And so should all projects, actually.

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written 8.6 years ago by WouterDeCoster

1 answer

The setup.py is made for python2. pip3 uses python3.

The fix might be easy (adapting the setup.py) but it's likely that there are more incompatibilities and you are better off using a Python2.7 installation or virtual environment.

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written 8.6 years ago by WouterDeCoster