cellprofiler_stardist.def

Bootstrap:docker
# use linux-amd64 ubuntu jammy
From:mambaorg/micromamba@sha256:e678de11f8a47f2811f051a1329a7910bfbe056a49c63152a761d83dec3e5c4e

%post
# get build tools needed for cellprofiler dependencies lacking wheels and wxPython
	apt update -y
	apt install -y gcc git build-essential libxxf86vm-dev libnotify-dev libsdl2-dev libgtk-3-dev libwebkit2gtk-4.0-dev

# create environment yaml file, it will be in the root of container for reference
	{
	echo 'name: cellprofiler'
	echo 'channels:'
	echo '  - conda-forge'
	echo 'dependencies:'
	echo '  - python =3.8'
	echo '  - openjdk =11'
	echo '  - boto3 >=1.12.28'
	echo '  - docutils =0.15.2'
	echo '  - h5py >=3.6.0,<3.7.dev0,<4'
	echo '  - imageio >=2.5'
	echo '  - inflect >=2.1,<7'
	echo '  - jinja2 >=2.11.2'
	echo '  - joblib >=0.13'
	echo '  - mahotas >=1.4'
	echo '  - matplotlib-base >=3.1.3,<4'
	echo '  - mysqlclient =1.4.6'
	echo '  - numpy >=1.20.1'
	echo '  - pillow >=7.1.0'
	echo '  - pyzmq >=22.3,<23.dev0'
	echo '  - sentry-sdk =0.18.0'
	echo '  - requests >=2.22'
	echo '  - scikit-image =0.18.3'
	echo '  - scikit-learn >=0.20,<1'
	echo '  - scipy =1.9.0'
	echo '  - future >=0.18.2'
	echo '  - psutil >=5.7.0'
	echo '  - six'
	echo '  - tifffile <2022.4.22'
	echo '  - stardist'
	echo ''
	echo '  - pip:'
	echo '    - https://extras.wxpython.org/wxPython4/extras/linux/gtk3/ubuntu-22.04/wxPython-4.2.1-cp38-cp38-linux_x86_64.whl'
	echo '    - cellprofiler==4.2.6'
	} > environment.yaml

# use micromamba to install dependencies from conda-forge and cellprofiler from pip
	micromamba create -f environment.yaml
# clean up unneeded conda files
	micromamba clean --all --yes

# create a CellProfiler plugins dir
    cd /opt
    git clone https://github.com/CellProfiler/CellProfiler-plugins.git

%runscript
#!/bin/bash
if [ -f "~/CellProfilerLocal.cfg" ]
then
	if cat CellProfilerLocal.cfg | grep -q PluginDirectoryCP4
	then
		echo "Plugin directory already set"
	else
		echo 'PluginDirectoryCP4=/opt/CellProfiler-plugins/active_plugins' >> ~/CellProfilerLocal.cfg
	fi
else
	{
    echo 'PreferencesVersion=1'
    echo 'Telemetry=0'
    echo 'Telemetry\ prompt=0'
	echo 'PluginDirectoryCP4=/opt/CellProfiler-plugins/active_plugins'
	} > ~/CellProfilerLocal.cfg
fi
eval "$(micromamba shell hook --shell bash)"
micromamba activate cellprofiler
cellprofiler