OptiType fails to run with the current setup

[armish]

@tavinathanson discovered this during his recent trials. Here is the error log of an attempt to run OptiType on a legit data set:

Traceback (most recent call last):
  File "<string>", line 114, in <module>
  File "/nfs-pool/biokepi/toolkit/biopam-kit/envs/optitype.1.0.0/lib/python2.7/site-packages/PyInstaller/loader/pyimod03_importers.py", line 389, in load_module
    exec(bytecode, module.__dict__)
  File "model.py", line 15, in <module>
  File "/nfs-pool/biokepi/toolkit/biopam-kit/envs/optitype.1.0.0/lib/python2.7/site-packages/PyInstaller/loader/pyimod03_importers.py", line 389, in load_module
    exec(bytecode, module.__dict__)
  File "site-packages/pyomo/environ/__init__.py", line 13, in <module>
  File "/nfs-pool/biokepi/toolkit/biopam-kit/envs/optitype.1.0.0/lib/python2.7/site-packages/PyInstaller/loader/pyimod03_importers.py", line 389, in load_module
    exec(bytecode, module.__dict__)
  File "site-packages/pyomo/core/__init__.py", line 10, in <module>
  File "/nfs-pool/biokepi/toolkit/biopam-kit/envs/optitype.1.0.0/lib/python2.7/site-packages/PyInstaller/loader/pyimod03_importers.py", line 389, in load_module
    exec(bytecode, module.__dict__)
  File "site-packages/pyomo/util/__init__.py", line 10, in <module>
  File "/nfs-pool/biokepi/toolkit/biopam-kit/envs/optitype.1.0.0/lib/python2.7/site-packages/PyInstaller/loader/pyimod03_importers.py", line 389, in load_module
    exec(bytecode, module.__dict__)
  File "site-packages/pyomo/util/_task.py", line 20, in <module>
ImportError: No module named pyutilib.workflow
OptiTypePipeline returned -1

Seems that there is something wrong with the way pyutilib and pyomo libraries are interacting, but we weren't able to trace the issue down to a specific cause.

[tavinathanson]

(Edit: had some comments here about #419 but just created a separate issue.)

[tavinathanson]

This is fixed with @armish's switch to OptiType via bioconda.