THIS REPO IS NO LONGER SUPPORTED OR MAINTAINED - PLEASE UTILIZE THE CONDA INSTALLATION INSTRUCTIONS FOR LINUX FOUND HERE:
https://github.com/CellProfiler/CellProfiler/wiki/Source-installation-(Linux)
This repo filled a need that has passed for the original use case, and the creators have unified their platform in a way that is much more accessible. Thanks for visiting.
Install script for CellProfiler v3.1.9 on Ubuntu 18.04.3 LTS(+) - bash, installs python3.6
proven to work on Ubuntu 18.04 and installs all dependencies. For support and queries, route to the Cellprofiler page on Github. This script is simply an installer to make it easier for users to get CellProfiler on their linux workstations with a supported version of python.
NOTE: AT THIS TIME UBUNTU 19.X/20.X IS NOT SUPPORTED (working on it)
at time of publication- cellprofiler is not supported on version 3.x for linux, and the modules "classify" and "classifypixelsunet" are not supported on linux. Or at least not officially. This script serves to rectify that oversight.
Note: I do not own, nor do I support, the plugins or software that this script installs. I simply bridge the gap between cellprofiler and linux (ubuntu). My script will make changes to your operating system, so I advise making a backup before running, and I offer no warranty, As-is standard agreement, not my fault, etc. (It's fine I just have to say it).
For code base support after installation, check the cellprofiler page: https://github.com/cellprofiler/cellprofiler
before you begin: $ sudo apt update && sudo apt upgrade -y (this is important so you can verify that apt isn't locked due to background updating before you start the install process)
- Clone this repo to your Target workstation desktop:
sudo git clone https://github.com/scotchman0/CellProfiler_Ubuntu_Installer.git
- enter the target folder and make the Install target file exectuable:
sudo chmod a+x ./CellProfiler_Install.sh
- Run the script with:
sudo ./CellProfiler_Install.sh
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There is a point after you start the script that will require you to edit ~/Cellprofiler/setup.py to lower the required python version from 3.7 to 3.6. You'll have to make the edit then press return to continue running the installer. (3.7 seems to throw many more errors than 3.6).
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Wait. The script takes up to 10 mins on less nice systems (a few mins on great systems) and up to an hour on a VM with 2gb ram. (mostly because wxPython build from binary takes FOREVER), and it was preferable to see the output rather than believe that the script was hanging for a full hour on "building wxPython from wheel..."
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The script will launch cellprofiler and you can call the app with "cellprofiler" in a terminal window from its install path.
Comments on code are explanatory enough (I hope) to explain why things are occurring and what lives where for better troubleshooting in the future.
NOTICE - some modules will not function correctly unless you call cellprofiler with SUDO or as root
$ sudo cellprofiler will enable unet module to run properly in your pipeline - issue#4
NOTES Submit some issue logs here if you run into trouble - usually the big issue is that Javabridge will claim to not be installed (but it is). It got installed in the wrong spot. There's a line that fixes this in the current build:
mv ~/.local/lib/python3.6/site-packages/* /usr/local/lib/python3.6/dist-packages/
you shouldn't need to do much with this, just know that it's happening (moving the javabridge install baseline into the correct spot).
You should also be made aware that this script will set your default python3 and python variable to python3.6 for ease of install. You can set these back to a different version by simply installing a later version of python (which will update the python3 symlink), or by manually editing the link file in /usr/local/bin/ with:
cd /usr/bin && rm ./python && ln -s python2.7 ./python cd /usr/bin && rm ./python3 && ln -s python3.7 ./python3
(edit the before line to whatever version you want "python" to summon - vs python3 summoning build of 3.5/3.7 etc)