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broadinstitute / oncotator

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Fixed README to compensate python3 syntax error. #372

Open soymintc opened 6 years ago

soymintc commented 6 years ago

The following error occurs when I followed the README to install oncotator in a virtual environment. I'd be better to create a virtualenv with python2:

File "/home/kwangsookim/oncoenv/lib/python3.4/site-packages/Oncotator-1.10.0.0.dev0-py3.4.egg/oncotator/index/gaf.py", line 90
    print j
          ^
SyntaxError: Missing parentheses in call to 'print'
LeeTL1220 commented 6 years ago

@alexbmp I cannot accept this pull request, since it would encourage users to skip running the create_oncotator_venv.sh script. Any fix would have to be in the codebase.

lbergelson commented 6 years ago

@alexbmp Maybe you could add the -v python2 option to create_oncotator_venv.sh instead of the README.

soymintc commented 6 years ago

@LeeTL1220 @lbergelson I see. I just added the python2 option -p python2 inside scripts/create_oncotator_venv.sh so that virtualenv based on python3 does not automatically create a python3 environment for oncotator. However, please not that many module tests still fail during Travis.