Again, some things have changed since 11.10.
The following has been tested on a fresh Ubuntu “server” installation, 15.04.
The goal of these instructions is to use packages provided by the Linux distribution wherever possible, and to install the rest in a non-obtrusive way in the user’s home directory (to avoid conflicts or unexpected behavior of the system). In other words: there is no excessive use of sudo here, as in many other how-to’s out there…
Prepare Ubuntu packages
First all packages that are available through Ubuntu’s own repositories will be installed. This includes Python itself, its required packages, git and Java:
sudo apt-get install —yes \
cython \
git \
openjdk-8-jdk \
python-h5py \
python-lxml \
python-matplotlib \
python-mysqldb \
python-pandas \
python-pip \
python-scipy \
python-skimage \
python-vigra \
python-wxgtk3.0 \
python-zmq
Install additional Python packages
Some of the required packages are not available through Ubuntu, so they have to be installed manually.
pip install —no-deps \
javabridge \
python-bioformats \
hmmlearn \
centrosome \
cellh5
Now there is one remaining package which has to be shown to be particularly nasty during installation while creating this how-to, that is prokaryote. My recommendation is to install it in verbose mode, so you can see what’s going on, especially as it has to retrieve a quite large JAR file (>130 MB) from github, which can sometimes be extremely slow.
pip install —no-deps -vvv prokaryote
Prepare the environment
export JAVA_HOME=”/usr/lib/jvm/java-8-openjdk-amd64”
export LD_LIBRARY_PATH=”$JAVA_HOME/jre/lib/amd64/server”
Get CellProfiler and run it
Beware that if you’re connected via ssh, make sure to enable X-forwarding (e.g. by using ssh -X for connecting) to be able to display CellProfiler’s GUI.
git clone https://github.com/CellProfiler/CellProfiler.git
cd CellProfiler/
python CellProfiler.py
Not (yet) covered: integration of Ilastik