Linux release

[antonkulaga]

Could you please publish Linux release?

[DavidStirling]

Unfortunately we don't currently have access to Linux machines for testing, and the variability between distributions can cause problems. Have you tried installing from source?

[antonkulaga]

There are instructions for cellprofiler, where are instructions for cellprofiler analyst?

[DavidStirling]

As far as I'm aware nobody has tried a Linux installation of CPA3 yet, so the wiki instructions are outdated. I'd suggest that you install Python 3.8, git clone the repository and run pip install -e ..

[antonkulaga]

I am having issues with the regular CellProfiler. Maybe you can make at least a conda-package for it, because your pip is half-broken in terms of dependencies. I kind of managed to make it partially work, but still getting errors https://github.com/CellProfiler/CellProfiler/issues/4415?fbclid=IwAR3i9vsnqIja_KEnnswATP9isUnSsiLnzCzQHNtczbzevTroB6W_iQyw7zU

[DavidStirling]

CellProfiler Linux instructions are still in need of improvement. That said, Analyst has far fewer dependencies so hopefully that should be less broken.

[andersla]

These are instructions I came up with when installing CellProfiler-Analyst on Ubuntu 20.04, I installed in a python venv to avoid conflicts with other python libs on the server, hope they can help:

# install dependencies from ubuntu repos
sudo apt-get update
sudo apt-get install -y \
    build-essential \
    default-libmysqlclient-dev \
    git \
    libgtk-3-dev \
    libnotify-dev \
    libsdl2-dev \
    libzmq3-dev \
    locales \
    openjdk-11-jdk-headless \
    python3-pip \
    python3-venv

# clone git-repo
git clone https://github.com/CellProfiler/CellProfiler-Analyst.git

# It is probably best to checkout a specific tag here,
git checkout 3.0.4

# enter cloned repo
cd CellProfiler-Analyst

# create and activete venv
python3 -m venv venv
source venv/bin/activate

# install pip depeendencies (not in requirements.txt)
pip install numpy

# add JAVA_HOME (needed py some pip packages, when building with wheel)
export JAVA_HOME=/usr/lib/jvm/java-11-openjdk-amd64

# build and compile Python dependencies and CellProfiler-Analyst
pip install -e .

To run the program you could create a simple bash-script CellProfiler-Analyst.sh activating venv and running main module

#!/usr/bin/env bash
source /**<install-dir>**/venv/bin/activate
python3 -m CellProfiler-Analyst

To remove program, just rm the CellProfiler-Analyst directory that also contains the Python venv directory

[andersla]

I added install instr. as a wiki page also: https://github.com/CellProfiler/CellProfiler-Analyst/wiki/Source-Installation-(Ubuntu-20.04)