Ubuntu 18.04
Beth Cimini edited this page Sep 14, 2020
·
9 revisions
Right now, due to an ongoing wx issue, CellProfiler on Ubuntu18 seems to only work when installed inside a venv OR when you build wx from scratch (which can be very slow). We will update the instructions when these issues resolve.
sudo apt update
sudo apt -y upgrade
sudo apt install -y make gcc build-essential libgtk-3-dev
sudo apt install -y python3.8-dev python3.8-venv python3-pip openjdk-11-jdk-headless default-libmysqlclient-dev libnotify-dev libsdl2-dev libwebkit2gtk-4.0-dev
#If and only if you are building your wxPython not from a wheel, you may need the following libraries:
#Otherwise, skip to the "in a venv" steps
sudo apt-get install -y \
freeglut3 \
freeglut3-dev \
libgl1-mesa-dev \
libglu1-mesa-dev \
libgstreamer-plugins-base1.0-dev \
libgtk-3-dev \
libgtk2.0-dev \
libjpeg-dev \
libnotify-dev \
libsdl2-dev \
libsm-dev \
libtiff-dev \
libwebkit2gtk-4.0-dev \
libwebkitgtk-dev \
libxtst-dev
export JAVA_HOME=/usr/lib/jvm/java-11-openjdk-amd64
export PATH=$PATH:/home/ubuntu/.local/bin
python3.8 -m pip install \
-f https://extras.wxpython.org/wxPython4/extras/linux/gtk3/ubuntu-18.04 \
wxPython==4.1.0
python3.8 -m pip install cellprofiler
## Otherwise, in a venv
python3.8 -m venv cellprofiler
source cellprofiler/bin/activate
export JAVA_HOME=/usr/lib/jvm/java-11-openjdk-amd64
export PATH=$PATH:/home/ubuntu/.local/bin
python3.8 -m pip install wheel
python3.8 -m pip install \
-f https://extras.wxpython.org/wxPython4/extras/linux/gtk3/ubuntu-18.04 \
wxPython==4.1.0
python3.8 -m pip install cellprofiler
- Linux
- MacOS M1 source installation
- macOS and OS X
- Opening CellProfiler on Mac OS 10.15.7
- Ubuntu 20.04
- Ubuntu 18.04
- Ubuntu 16.04 LTS
- Windows
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- Arch Linux
- CellProfiler as a Python package
- Interfacing with other software
- OMERO: Accessing images from CellProfiler
- Getting started using CellProfiler from the command line
- Adapting CellProfiler to a LIMS environment
- s3
- Plugins
- RunImageJMacro
- Orientation to CellProfiler code
- Module structure and data storage retrieval
- Concurrency Model - Analysis Mode and ZMQ Interfaces
- Issues