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I recently checked out a fresh copy of CP2 from the git repo according to instructions https://github.com/CellProfiler/CellProfiler/wiki/CellProfiler-Developer%27s-version-installation-for-Linux .

After installing all the dependencies listed on the page, I tried running cp2 but python complains about a missing package:

lee@silvercomet:~/school/cell_profiler/CellProfiler$ python CellProfiler.py Traceback (most recent call last): File "CellProfiler.py", line 34, in <module> import zmq ImportError: No module named zmq

Neither pip nor easy_install knows anything about zmq. What is it? And where can I get it?

Here’s my version info

lee@silvercomet:~/school/cell_profiler/CellProfiler$ svn info Path: . URL: https://github.com/CellProfiler/CellProfiler.git/trunk Repository Root: https://github.com/CellProfiler/CellProfiler.git Repository UUID: cf5fdc03-9a43-06a6-f4ba-ce57b7db7bff Revision: 11009 Node Kind: directory Schedule: normal Last Changed Author: braymp Last Changed Rev: 11009 Last Changed Date: 2013-11-18 15:23:01 -0500 (Mon, 18 Nov 2013)

Thanks,


   
    Nevermind, got it from my local debian mirror.
   
   
    For debian based systems, there are a couple of dependencies which are not listed on the linux CP2 installation wiki (
    
     https://github.com/CellProfiler/CellProfiler/wiki/CellProfiler-Developer%27s-version-installation-for-Linux
    
    ) that are available as packages (at least for versions >= 7.0 / Wheezy).  Are lay githubbers allowed to edit the wiki?  It would be useful for future linux users.
   
   
    Thanks,
   
   
    Hi Lee,
   
   
    The wiki isn’t open for general editing, but if you let me know what to change, I can put it in.
   
   
    As a side note: Our group has made some progress on creating CellProfiler RPMs for RedHat, so stay tuned…
   
   
    Regards,
    

    -Mark
   
   
    [quote=“mbray”]Hi Lee,
   
   
    The wiki isn’t open for general editing, but if you let me know what to change, I can put it in.[/quote]
   
   
    Ok, sure.  The two groups of required packages which aren’t currently listed for debian based systems are h5py oriented packages, and zmq oriented packages.  For h5py, the following debian packages should be installed (via aptitude, apt, or synaptic):
   
   
    python-h5py
    

    hdf5-helpers
    

    libhdf5-dev
    

    libjpeg8-dev
   
   
    For zmq, the following debian packages should be installed:
   
   
    libpgm-5.1-0
    

    libzmq1
    

    python-zmq
   
   
    These package should be added to the list of debian (or derivatives such as ubuntu) to be installed.  The current list is in numbered list item
    
     9
    
    , under the header
    
     Option 2
    
    on the wiki page
    
     https://github.com/CellProfiler/CellProfiler/wiki/CellProfiler-Developer%27s-version-installation-for-Linux#option-2-install-all-the-individual-libraries-and-dependencies
    
    .
   
   
    Thanks again for working on making CP2 easier to install for us linux folks,
   
   
    p.s here’s my sources.list
   
   
    [code]deb
    
     http://mirror.csclub.uwaterloo.ca/debian/
    
    wheezy main contrib non-free
    

    deb-src
    
     http://mirror.csclub.uwaterloo.ca/debian/
    
    wheezy main contrib non-free
    
     #Added
    
    by software-properties
   
   
    deb
    
     http://security.debian.org/
    
    wheezy/updates main contrib non-free
    

    deb-src
    
     http://security.debian.org/
    
    wheezy/updates main contrib non-free
    
     #Added
    
    by software-properties
   
   
    for scipy-numpy, scikit-learn packages
   
   
    deb
    
     http://neuro.debian.net/debian
    
    data main contrib non-free
   
   
    deb-src
    
     http://neuro.debian.net/debian
    
    data main contrib non-free
   
   
    deb
    
     http://neuro.debian.net/debian
    
    wheezy main contrib non-free
   
   
    deb-src
    
     http://neuro.debian.net/debian
    
    wheezy main contrib non-free
   
   
    [/code]

for scipy-numpy, scikit-learn packages

deb-src http://neuro.debian.net/debian data main contrib non-free

deb-src http://neuro.debian.net/debian wheezy main contrib non-free