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Source installation (Ubuntu 16.04 LTS)
This procedure has been confirmed to work on a clean install of Ubuntu 16.04. First install system prerequisites for CellProfiler with apt. You will have to confirm the list of installed packages:
$ sudo apt-get update $ sudo apt-get upgrade $ sudo apt-get install \ build-essential \ cython \ git \ libmysqlclient-dev \ libhdf5-dev \ libxml2-dev \ libxslt1-dev \ openjdk-8-jdk \ python-dev \ python-pip \ python-h5py \ python-matplotlib \ python-mysqldb \ python-scipy \ python-numpy \ python-vigra \ python-wxgtk3.0 \ python-zmq
Checkout the CellProfiler sources:
$ git clone https://github.com/CellProfiler/CellProfiler.git $ cd CellProfiler
Its possible to use a specific branch or tag of CellProfiler. The latest stable version is in branch 'stable', or specific versions can be found in tags. I.e. to use the latest stable, use:
$ git checkout stable
or to use version 2.2.0, use:
$ git checkout 2.2.0
Finally when you have checked out the version you want, you are ready to start the compile / install of python dependencies.
$ sudo pip install --editable .
Alternatively, you can install CellProfiler into your home directory (preferred):
$ pip install --user --editable .
If you get an error
ImportError: No module named Cython.Build run
pip install --upgrade cython
When using pip with
--user, it will install CellProfiler and its dependencies in the platform-specific user install directory. It is possible to get the install directory from Python itself using the site module. This may be something like
$HOME/.local, so the packages may be installed in
$ python -m site --user-base
Add this directory to your PATH environment variable to start pip-installed packages:
$ export PATH="$HOME/.local/bin:$PATH"
will run CellProfiler.
Issues and Workarounds
There is an issue in 2.2.0 that breaks the java bindings in prokaryote. To work around the issue, its sufficient to re-install prokaryote from the CellProfiler source directory:
pip uninstall prokaryote pip install prokaryote
If you get this error:
... File "/tmp/easy_install-YiEaoP/javabridge-1.0.15/setup.py", line 137, in ext_modules ] File "/usr/lib/python2.7/posixpath.py", line 122, in dirname i = p.rfind('/') + 1 AttributeError: 'NoneType' object has no attribute 'rfind'
Be sure to use java 8:
sudo update-alternatives --config java
pip uninstall cellprofiler