Source installation (Ubuntu 15.10)

This procedure has been confirmed to work on a clean install of Ubuntu 15.10. First you will need to install all prerequisites of CellProfiler as outlined on the website https://github.com/CellProfiler/CellProfiler/wiki/Source-installation-(Ubuntu-15.10). Then follow the instructions below.

Install system prerequisites for CellProfiler Analyst with apt. You will have to confirm the list of installed packages:

$ sudo apt-get update
$ sudo apt-get upgrade
$ sudo apt-get install \
    python-mysqldb \
    python-sqlite \
    python-seaborn \
    python-sklearn \
    python-mock \
    python-pandas

Now checkout the CellProfiler Analyst sources where the install should reside. This example will check out to /opt:

$ sudo git clone https://github.com/CellProfiler/CellProfiler-Analyst.git /opt/CellProfiler-Analyst
$ cd /opt/CellProfiler-Analyst/

Its possible to use a specific branch or tag of CellProfiler Analyst. 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 2.2.1, use:

$ git checkout tags/2.2.1

Finally when you have checked out the version you want, you are ready to start the compile / install of python dependencies. This will install python packages and a CellProfiler start script to sub-directories of /usr/local/. To avoid installing with sudo, the easiest solution is to temporarily allow write access to the required install directories using:

$ sudo chmod -R o+w \
    /usr/local/lib/python2.7/dist-packages \
    /usr/local/bin

Then install the remaining Python package dependencies:

$ pip install verlib

Finally revoke the write permissions on the /usr/local sub-directories again:

$ sudo chmod -R o-w \
    /usr/local/lib/python2.7/dist-packages \
    /usr/local/bin

You can then run CellProfiler Analyst, which has been installed in /opt/CellProfiler-Analyst, as a normal user. Start it via python manually:

$ cd /opt/CellProfiler-Analyst/
$ python CellProfiler-Analyst.py

Uninstalling CellProfiler Analyst and dependencies

To uninstall CellProfiler, delete the source directory at /opt/CellProfiler-Analyst. Optionally, you can also remove the python dependency packages at /usr/lib/python2.7/dist-packages, but beware that python dependency packages might be used by other python tools as well! The full instructions are:

rm -fr /opt/CellProfiler-Analyst
rm -fr /usr/lib/python2.7/dist-packages/*