CellProfiler development installation on Ubuntu 20.04

cellprofiler-dev-installation-ubuntu-20-04.md

CellProfiler development installation on Ubuntu 20.04

Guide created February 2021

1. Install dependencies

Install these dependencies

sudo apt update
sudo apt -y upgrade
sudo apt install -y make gcc build-essential libgtk-3-dev
sudo apt-get install -y python3-pip openjdk-11-jdk-headless default-libmysqlclient-dev libnotify-dev libsdl2-dev
#If and only if you are building your wxPython not from a wheel, you may need the following libraries:
#Otherwise, skip to the "export" steps
sudo apt-get install -y \
                freeglut3 \
                freeglut3-dev \
                libgl1-mesa-dev \
                libglu1-mesa-dev \
                libgstreamer-plugins-base1.0-dev \
                libgtk-3-dev \
                libjpeg-dev \
                libnotify-dev \
                libsdl2-dev \
                libsm-dev \
                libtiff-dev \
                libwebkit2gtk-4.0-dev \
                libxtst-dev

2. Add the java path to $JAVA_HOME and restart your terminal

sudo nano .bashrc

Add this line to your .bashrc file: export JAVA_HOME=/usr/lib/jvm/java-11-openjdk-amd64

Restart your terminal for this change to take effect.

3. Install libwebkitgtk

sudo nano /etc/apt/sources.list

Add this line to your /etc.apt/sources.list: deb http://cz.archive.ubuntu.com/ubuntu bionic main universe

Now you will be able to install libwebkitgtk:

sudo apt-get update
sudo apt-get install libwebkitgtk-1.0-0 

4. Create your conda development environment

We create a Python 3.8 conda environment, and install wxPython and javabridge into it.

conda create -n cellprofiler-dev python=3.8 pip
conda activate cellprofiler-dev
conda install wxPython python-javabridge

5. Fork/clone the CellProfiler repository

Fork/clone the CellProfiler repository if you don't already have this.

git clone git@github.com:CellProfiler/CellProfiler.git
cd CellProfiler

6. Update the pinned numpy version

Must change pinned numpy version to "numpy==1.20.1" in CellProfiler setup.py (an upgrade from the current numppy pinned version 1.19.3)

nano setup.py

7. Install CellProfiler from the master branch

Editable installation of CellProfiler:

cd GitHub/CellProfiler
pip install -e .

8. Install cellprofiler-core from the master branch

Fork/clone CellProfiler core, if you don't already have this.

cd ..
git clone git@github.com:CellProfiler/core.git
cd core

Editable installation of CellProfiler core:

pip uninstall cellprofiler-core
pip install -e .

9. OPTIONAL - Install centrosome fromt the master branch

Fork/clone centrosome, if you don't already have this.

cd ..
git clone git@github.com:CellProfiler/centrosome.git
cd centrosome

Editable installation of centrosome:

pip uninstall centrosome
pip install -e .

10. Check everything is working properly

$ python
>>> import wx
>>> import javabridge
>>> # there should be no import errors

$ cellprofiler
$ # you should see the main CellProfiler window open