Installation of Cellprofiler-problems with ilastik and wx modules

Hi dear Cellprofiler Community,
I want to download the cellprofiler because I need it in my downloaded workflow for knime 3.5.3 (


I first loaded the example workflow for cellprofiler-colocalization as well as cellprofiler-comet assay workflow in knime and made the changes as said by: (https://www.knime.com/community/cellprofiler) but as I wanted to execute the cellprofiler pipeline excecuter node I got the following error with comet assay workflow(“unexpected charachter 67”) and no error with colocalization workflow but it works for hours and days with no results or errors. Since I did not installed the cell profiler package I started working on that:

so in the process of installation of CellProfiler on Ubuntu 14.04 based of link (https://github.com/CellProfiler/CellProfiler/wiki/Source-Installation-(Ubuntu-14.04-LTS)) I need to go through following steps:

sudo apt-get update
sudo apt-get upgrade
sudo apt-get install \
  cython             \
  git                \
  libmysqlclient-dev \
  libhdf5-dev        \
  libxml2-dev        \
  libxslt1-dev       \
  openjdk-7-jdk      \
  python-dev         \
  python-pip         \
  python-h5py        \
  python-matplotlib  \
  python-mysqldb     \
  python-scipy       \
  python-vigra       \
  python-wxgtk2.8    \
  python-zmq
sudo pip install --upgrade cython
sudo pip install dask
sudo pip install --upgrade six
sudo git clone https://github.com/CellProfiler/CellProfiler.git /opt/CellProfiler
sudo git checkout stable
cd /opt/CellProfiler/
sudo pip install --editable . --process-dependency-links
sudo pip uninstall prokaryote
sudo pip install prokaryote
sudo pip install javabridge

which I completed. and then

$ cd /opt/CellProfiler
$ python CellProfiler.py

here I get the following error:

Exception fetching new version information from http://cellprofiler.org/CPupdate.html: <urlopen error [Errno -2] Name or service not known>
Uncaught exception in CellProfiler.py
Traceback (most recent call last):
  File "/opt/CellProfiler/cellprofiler/__main__.py", line 226, in main
    pipeline_path = pipeline_path)
  File "/opt/CellProfiler/cellprofiler/cellprofilerapp.py", line 24, in __init__
    super(CellProfilerApp, self).__init__(*args, **kwargs)
  File "/usr/lib/python2.7/dist-packages/wx-2.8-gtk2-unicode/wx/_core.py", line 7981, in __init__
    self._BootstrapApp()
  File "/usr/lib/python2.7/dist-packages/wx-2.8-gtk2-unicode/wx/_core.py", line 7555, in _BootstrapApp
    return _core_.PyApp__BootstrapApp(*args, **kwargs)
  File "/opt/CellProfiler/cellprofiler/cellprofilerapp.py", line 34, in OnInit
    from cellprofiler.gui.cpframe import CPFrame
  File "/opt/CellProfiler/cellprofiler/gui/cpframe.py", line 17, in <module>
    from cellprofiler.modules import get_data_tool_names, instantiate_module
ImportError: No module named modules
Failed to stop Ilastik
Traceback (most recent call last):
  File "CellProfiler.py", line 4, in <module>
    cellprofiler.__main__.main()
  File "/opt/CellProfiler/cellprofiler/__main__.py", line 226, in main
    pipeline_path = pipeline_path)
  File "/opt/CellProfiler/cellprofiler/cellprofilerapp.py", line 24, in __init__
    super(CellProfilerApp, self).__init__(*args, **kwargs)
  File "/usr/lib/python2.7/dist-packages/wx-2.8-gtk2-unicode/wx/_core.py", line 7981, in __init__
    self._BootstrapApp()
  File "/usr/lib/python2.7/dist-packages/wx-2.8-gtk2-unicode/wx/_core.py", line 7555, in _BootstrapApp
    return _core_.PyApp__BootstrapApp(*args, **kwargs)
  File "/opt/CellProfiler/cellprofiler/cellprofilerapp.py", line 34, in OnInit
    from cellprofiler.gui.cpframe import CPFrame
  File "/opt/CellProfiler/cellprofiler/gui/cpframe.py", line 17, in <module>
    from cellprofiler.modules import get_data_tool_names, instantiate_module
ImportError: No module named modules

although in ls I can see Modules. before that I had also the error in finding Ilastik Module (which I installed as well as copied the python directory in my cellprofiler directory and also the error regarding matplot :slight_smile:

/opt/CellProfiler$ python CellProfiler.py
ilastik import: failed to import the ilastik. Please follow the instructions on
    "ilastikdotorg" to install ilastik
Traceback (most recent call last):
  File "/opt/CellProfiler/cellprofiler/modules/classifypixels.py", line 71, in <module>
    from ilastik.core.dataMgr import DataMgr, DataItemImage
ImportError: No module named ilastik.core.dataMgr
ilastik import: failed to import the ilastik. Please follow the instructions on
                          "lastik.." to install ilastik
Traceback (most recent call last):
  File "/opt/CellProfiler/cellprofiler/modules/ilastik_pixel_classification.py", line 70, in <module>
    import ilastik_main
ImportError: No module named ilastik_main
Could not load cellprofiler.modules.exporttocellh5
Traceback (most recent call last):
  File "/opt/CellProfiler/cellprofiler/modules/__init__.py", line 294, in add_module
    m = __import__(mod, globals(), locals(), ['__all__'], 0)
  File "/opt/CellProfiler/cellprofiler/modules/exporttocellh5.py", line 29, in <module>
    import cellh5
  File "/usr/local/lib/python2.7/dist-packages/cellh5/__init__.py", line 12, in <module>
    from cellh5 import *
  File "/usr/local/lib/python2.7/dist-packages/cellh5/cellh5.py", line 18, in <module>
    import matplotlib.pyplot as plt
  File "/usr/local/lib/python2.7/dist-packages/matplotlib/pyplot.py", line 115, in <module>
    _backend_mod, new_figure_manager, draw_if_interactive, _show = pylab_setup()
  File "/usr/local/lib/python2.7/dist-packages/matplotlib/backends/__init__.py", line 62, in pylab_setup
    [backend_name], 0)
  File "/usr/local/lib/python2.7/dist-packages/matplotlib/backends/backend_wxagg.py", line 10, in <module>
    from . import wx_compat as wxc
  File "/usr/local/lib/python2.7/dist-packages/matplotlib/backends/wx_compat.py", line 32, in <module>
    raise ImportError(missingwx)
ImportError: Matplotlib backend_wx and backend_wxagg require wxPython>=2.9
could not load these modules: cellprofiler.modules.exporttocellh5
Uncaught exception in CellProfiler.py
Traceback (most recent call last):
  File "/opt/CellProfiler/cellprofiler/__main__.py", line 226, in main
    pipeline_path = pipeline_path)
  File "/opt/CellProfiler/cellprofiler/cellprofilerapp.py", line 24, in __init__
    super(CellProfilerApp, self).__init__(*args, **kwargs)
  File "/usr/lib/python2.7/dist-packages/wx-2.8-gtk2-unicode/wx/_core.py", line 7981, in __init__
    self._BootstrapApp()
  File "/usr/lib/python2.7/dist-packages/wx-2.8-gtk2-unicode/wx/_core.py", line 7555, in _BootstrapApp
    return _core_.PyApp__BootstrapApp(*args, **kwargs)
  File "/opt/CellProfiler/cellprofiler/cellprofilerapp.py", line 34, in OnInit
    from cellprofiler.gui.cpframe import CPFrame
  File "/opt/CellProfiler/cellprofiler/gui/cpframe.py", line 19, in <module>
    from cellprofiler.gui.pipelinelistview import PipelineListView
  File "/opt/CellProfiler/cellprofiler/gui/pipelinelistview.py", line 27, in <module>
    from cellprofiler.gui.cpfigure import window_name, find_fig
  File "/opt/CellProfiler/cellprofiler/gui/cpfigure.py", line 18, in <module>
    import matplotlib.backends.backend_wxagg
  File "/usr/local/lib/python2.7/dist-packages/matplotlib/backends/backend_wxagg.py", line 10, in <module>
    from . import wx_compat as wxc
  File "/usr/local/lib/python2.7/dist-packages/matplotlib/backends/wx_compat.py", line 32, in <module>
    raise ImportError(missingwx)
ImportError: Matplotlib backend_wx and backend_wxagg require wxPython>=2.9
Failed to stop Ilastik
Exception fetching new version information from http://cellprofiler.org/CPupdate.html: <urlopen error [Errno -2] Name or service not known>

with /opt/CellProfiler$ pip freeze I get following:

amqp==2.3.2
ansible==1.7.2
apt-xapian-index==0.45
backports.functools-lru-cache==1.5
beautifulsoup4==4.2.1
boto==2.20.1
boto3==1.8.3
botocore==1.11.3
cell==0.0.3
cellh5==1.3.0
-e git+https://github.com/CellProfiler/CellProfiler.git@e07291ca85423ee1e7708b9458f5875c7b13b888#egg=CellProfiler
centrosome==1.0.9
chardet==2.0.1
chemfp===1.1p1
cinfony==1.2
colorama==0.2.5
command-not-found==0.3
contextlib2==0.5.5
cvxopt==1.1.4
cycler==0.10.0
Cython==0.28.5
dask==0.18.2
debtagshw==0.1
decorator==3.4.0
defer==1.0.6
dirspec==13.10
docutils==0.11
future==0.16.0
futures==3.2.0
h5py==2.2.1
hmmlearn==0.2.0
html5lib==0.999
httplib2==0.8
inflect==1.0.0
ipython==1.2.1
javabridge==1.0.17
Jinja2==2.7.2
jmespath==0.9.3
joblib==0.7.1
JPype==0.5.4.2
kiwisolver==1.0.1
kombu==4.2.1
lxml==3.3.3
mahotas==1.4.4
MarkupSafe==0.18
matplotlib==2.2.3
MySQL-python==1.2.3
mysqlclient==1.3.13
nose==1.3.1
numexpr==2.2.2
numpy==1.11.0
oauthlib==0.6.1
oneconf==0.3.7.14.4.1
openbabel==1.7
openpyxl==1.7.0
PAM==0.4.2
pandas==0.13.1
paramiko==1.10.1
patsy==0.2.1
pexpect==3.1
Pillow==2.3.0
piston-mini-client==0.7.5
ply==3.4
Pmw==1.3.2
profiler==0.1.0
prokaryote==2.4.0
protobuf==3.0.0b2
psutil==1.2.1
py==1.4.20
pychecker==0.8.19
pycrypto==2.6.1
pycups==1.9.66
pycurl==7.19.3
Pygments==1.6
pygobject==3.12.0
PyHyphen==1.0b1
pyinotify==0.9.4
Pymacs==0.23
pymol==1.7.0.0
PyOpenGL==3.0.2
pyOpenSSL==0.13
pyparsing==2.0.1
Pypubsub==4.0.0
pyserial==2.6
pysmbc==1.0.14.1
pytest==2.5.1
python-apt===0.9.3.5ubuntu3
python-bioformats==1.4.0
python-dateutil==2.7.3
python-debian===0.1.21-nmu2ubuntu2
pytz==2012rc0
pyxdg==0.25
PyYAML==3.10
pyzmq==15.3.0
raven==6.9.0
reportlab==3.0
requests==2.2.1
roman==2.0.0
s3transfer==0.1.13
scikit-image==0.9.3
scikit-learn==0.14.1
scipy==0.13.3
sessioninstaller==0.0.0
simplegeneric==0.8.1
simplejson==3.3.1
six==1.11.0
software-center-aptd-plugins==0.0.0
ssh-import-id==3.21
statsmodels==0.5.0
style==1.1.0
subprocess32==3.5.2
tables==3.1.1
tensorflow==0.9.0
tornado==3.1.1
Twisted-Core==13.2.0
Twisted-Web==13.2.0
typing==3.6.6
update==0.0.1
urllib3==1.23
vboxapi==1.0
vine==1.1.4
virtualenv==1.11.4
wxPython==2.8.12.1
wxPython-common==2.8.12.1
xlrd==0.9.2
xlwt==0.7.5
zope.interface==4.0.5

I tried to upgrade wxPython gtk to version 3 but I get the message unable to locate the file and it seems impossible.( Found existing installation: wxPython 2.8.12.1
Cannot uninstall ‘wxPython’. It is a distutils installed project and thus we cannot accurately determine which files belong to it which would lead to only a partial uninstall.)
with sudo pip install -Iv wxPython==4.0.3 I get after a few minutes and having all the files compiled the followi Command ‘"/usr/bin/python" /tmp/pip-install-ljPuRI/wxPython/bin/waf-2.0.7 --wx_config=/tmp/pip-install-ljPuRI/wxPython/build/wxbld/gtk3/wx-config --gtk3 --python="/usr/bin/python" --out=build/waf/2.7/gtk3 configure build ’ failed with exit code 1.
Finished command: build_py (5m2.258s)
Finished command: build (6m57.802s)
Command ‘"/usr/bin/python" -u build.py build’ failed with exit code 1.
error
Cleaning up…
Removing source in /tmp/pip-install-ljPuRI/wxPython
Removed build tracker ‘/tmp/pip-req-tracker-ce2lAI’
Command "/usr/bin/python -u -c "import setuptools, tokenize;file=’/tmp/pip-install-ljPuRI/wxPython/setup.py’;f=getattr(tokenize, ‘open’, open)(file);code=f.read().replace(’\r\n’, ‘\n’);f.close();exec(compile(code, file, ‘exec’))" install --record /tmp/pip-record-sEyoX3/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-install-ljPuRI/wxPython/
Exception information:
Traceback (most recent call last):
File “/usr/local/lib/python2.7/dist-packages/pip/_internal/basecommand.py”, line 141, in main
status = self.run(options, args)
File “/usr/local/lib/python2.7/dist-packages/pip/_internal/commands/install.py”, line 347, in run
use_user_site=options.use_user_site,
File “/usr/local/lib/python2.7/dist-packages/pip/_internal/req/init.py”, line 49, in install_given_reqs
**kwargs
File “/usr/local/lib/python2.7/dist-packages/pip/_internal/req/req_install.py”, line 972, in install
spinner=spinner,
File “/usr/local/lib/python2.7/dist-packages/pip/_internal/utils/misc.py”, line 701, in call_subprocess
% (command_desc, proc.returncode, cwd))
InstallationError: Command “/usr/bin/python -u -c “import setuptools, tokenize;file=’/tmp/pip-install-ljPuRI/wxPython/setup.py’;f=getattr(tokenize, ‘open’, open)(file);code=f.read().replace(’\r\n’, ‘\n’);f.close();exec(compile(code, file, ‘exec’))” install --record /tmp/pip-record-sEyoX3/install-record.txt --single-version-externally-managed --compile” failed with error code 1 in /tmp/pip-install-ljPuRI/wxPython/
There was an error checking the latest version of pip
Traceback (most recent call last):
File “/usr/local/lib/python2.7/dist-packages/pip/_internal/utils/outdated.py”, line 90, in pip_version_check
state = SelfCheckState(cache_dir=options.cache_dir)
File “/usr/local/lib/python2.7/dist-packages/pip/_internal/utils/outdated.py”, line 25, in init
self.statefile_path = os.path.join(cache_dir, “selfcheck.json”)
File “/usr/lib/python2.7/posixpath.py”, line 77, in join
elif path == ‘’ or path.endswith(’/’):
AttributeError: ‘NoneType’ object has no attribute ‘endswith’
ng error message:

I guess I am too confused and I am trying a lot of different processes together, that I lost focus. Can somebody helps me what steps should I take to work with comet assay workflow in knime and to be able to run the cellprofiler node in knime? and to install cellprofiler itself ?
I do not know where I am stuck?
best
Tannaz