Runipy using the wrong python

runipy_python_version_issues.txt

[obotvinnik@tscc-1-51 ~]$ export PYTHONPATH=$HOME/anaconda/lib/python2.7/site-packages/:$PYTHONPATH
[obotvinnik@tscc-1-51 ~]$ echo $PYTHONPATH
/home/obotvinnik/anaconda/lib/python2.7/site-packages/:/opt/sdsc/lib/:/opt/scar/lib/::/home/obotvinnik/local/lib/python2.7/site-packages/
[obotvinnik@tscc-1-51 ~]$ time ~/anaconda/bin/runipy /projects/ps-yeolab/obotvinnik/singlecell_pnms/notebooks/01_notebooks/00_chronological_order/041_translate_isoforms_to_protein_products_for_runipy_se.ipynb /projects/ps-yeolab/obotvinnik/singlecell_pnms/notebooks/01_notebooks/00_chronological_order/041_translate_isoforms_to_protein_products_for_runipy_se_runipy_output.ipynb
02/07/2017 08:23:59 AM INFO: Reading notebook /projects/ps-yeolab/obotvinnik/singlecell_pnms/notebooks/01_notebooks/00_chronological_order/041_translate_isoforms_to_protein_products_for_runipy_se.ipynb
Traceback (most recent call last):
  File "/projects/ps-yeolab/software/Anaconda_2.0.1_150511/lib/python2.7/runpy.py", line 151, in _run_module_as_main
    mod_name, loader, code, fname = _get_module_details(mod_name)
  File "/projects/ps-yeolab/software/Anaconda_2.0.1_150511/lib/python2.7/runpy.py", line 101, in _get_module_details
    loader = get_loader(mod_name)
  File "/projects/ps-yeolab/software/Anaconda_2.0.1_150511/lib/python2.7/pkgutil.py", line 464, in get_loader
    return find_loader(fullname)
  File "/projects/ps-yeolab/software/Anaconda_2.0.1_150511/lib/python2.7/pkgutil.py", line 474, in find_loader
    for importer in iter_importers(fullname):
  File "/projects/ps-yeolab/software/Anaconda_2.0.1_150511/lib/python2.7/pkgutil.py", line 430, in iter_importers
    __import__(pkg)
  File "/home/obotvinnik/anaconda/lib/python2.7/site-packages/IPython/__init__.py", line 49, in <module>
    from .terminal.embed import embed
  File "/home/obotvinnik/anaconda/lib/python2.7/site-packages/IPython/terminal/embed.py", line 16, in <module>
    from IPython.core.interactiveshell import DummyMod
  File "/home/obotvinnik/anaconda/lib/python2.7/site-packages/IPython/core/interactiveshell.py", line 31, in <module>
    from pickleshare import PickleShareDB
  File "/home/obotvinnik/anaconda/lib/python2.7/site-packages/pickleshare.py", line 41, in <module>
    from path import path as Path
  File "/home/obotvinnik/anaconda/lib/python2.7/site-packages/path.py", line 126, in <module>
    except pkg_resources.DistributionNotFound:
NameError: name 'pkg_resources' is not defined
^CTraceback (most recent call last):
  File "/home/obotvinnik/anaconda/bin/runipy", line 6, in <module>
    sys.exit(runipy.main.main())
  File "/home/obotvinnik/anaconda/lib/python2.7/site-packages/runipy/main.py", line 153, in main
    nb, args.pylab, args.matplotlib, profile_dir, working_dir
  File "/home/obotvinnik/anaconda/lib/python2.7/site-packages/runipy/notebook_runner.py", line 106, in __init__
    self.kc.wait_for_ready()
  File "/home/obotvinnik/anaconda/lib/python2.7/site-packages/jupyter_client/blocking/client.py", line 22, in wait_for_ready
^X    msg = self.shell_channel.get_msg(block=True)
  File "/home/obotvinnik/anaconda/lib/python2.7/site-packages/jupyter_client/blocking/channels.py", line 50, in get_msg
    ready = self.socket.poll(timeout)
  File "/home/obotvinnik/anaconda/lib/python2.7/site-packages/zmq/sugar/socket.py", line 503, in poll
    evts = dict(p.poll(timeout))
  File "/home/obotvinnik/anaconda/lib/python2.7/site-packages/zmq/sugar/poll.py", line 99, in poll
    return zmq_poll(self.sockets, timeout=timeout)
  File "zmq/backend/cython/_poll.pyx", line 115, in zmq.backend.cython._poll.zmq_poll (zmq/backend/cython/_poll.c:1705)
  File "zmq/backend/cython/checkrc.pxd", line 12, in zmq.backend.cython.checkrc._check_rc (zmq/backend/cython/_poll.c:2084)
KeyboardInterrupt
^Z
[2]+  Stopped                 ~/anaconda/bin/runipy /projects/ps-yeolab/obotvinnik/singlecell_pnms/notebooks/01_notebooks/00_chronological_order/041_translate_isoforms_to_protein_products_for_runipy_se.ipynb /projects/ps-yeolab/obotvinnik/singlecell_pnms/notebooks/01_notebooks/00_chronological_order/041_translate_isoforms_to_protein_products_for_runipy_se_runipy_output.ipynb

real    0m34.255s
user    0m0.000s
sys     0m0.001s
[obotvinnik@tscc-1-51 ~]$ ipython --version
4.1.1