FRED-2 / OptiType

Precision HLA typing from next-generation sequencing data

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Installation problem with pyomo module

Elisa89m opened this issue · comments

Hi,
I'm trying to install Optitype but I have some problem with pyomo module, when I'm trying to use Optitype it returns this error:

Traceback (most recent call last):
  File "/PATH/anaconda3/envs/python2_env/bin/pyomo", line 4, in <module>
    import pyomo.scripting.pyomo_main
  File "/PATH/anaconda3/envs/python2_env/lib/python2.7/site-packages/pyomo/scripting/__init__.py", line 14, in <module>
    import pyomo.scripting.pyomo_command
  File "/PATH/anaconda3/envs/python2_env/lib/python2.7/site-packages/pyomo/scripting/pyomo_command.py", line 25, in <module>
    import pyomo.scripting.util
  File "/PATH/anaconda3/envs/python2_env/lib/python2.7/site-packages/pyomo/scripting/util.py", line 65, in <module>
    from pyomo.opt import ProblemFormat
  File "/PATH/anaconda3/envs/python2_env/lib/python2.7/site-packages/pyomo/opt/__init__.py", line 14, in <module>
    from pyomo.opt.base import *
  File "/PATH/anaconda3/envs/python2_env/lib/python2.7/site-packages/pyomo/opt/base/__init__.py", line 14, in <module>
    from pyomo.opt.base.convert import *
  File "/PATH/anaconda3/envs/python2_env/lib/python2.7/site-packages/pyomo/opt/base/convert.py", line 16, in <module>
    from pyomo.opt.base.formats import guess_format
  File "/PATH/anaconda3/envs/python2_env/lib/python2.7/site-packages/pyomo/opt/base/formats.py", line 16, in <module>
    from pyutilib.enum import Enum
  File "/home/manager/.local/lib/python2.7/site-packages/pyutilib/enum/__init__.py", line 18, in <module>
    package) that supersedes this library.""")
ImportError: pyutilib.enum has been removed.

Python 3 now has an enum implementation in the standard library (also
available for older Python versions as the third-party enum34 PyPI
package) that supersedes this library.

Reading on internet it seems that this problem could be due to the python version but I need to install it under python2.7 as required from Optitype.
Can you help me? Is there a solution for this error?
I tried also to updated pyomo version even if optitype requires an older one.

Thank you in advance for your time.

Elisa

you need to specify the exact pyomo version (as in the readme).
pip install "pyomo==4.2"