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postBuild
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postBuild
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# Install Cytomine python client
pip install https://github.com/Cytomine-ULiege/Cytomine-python-client/archive/master.zip
# Install Neubias-W5-Utilities (annotation exporter, compute metrics, helpers,...)
git clone https://github.com/Neubias-WG5/neubiaswg5-utilities.git
cd neubiaswg5-utilities
pip install .
# install utilities binaries
chmod +x bin/*
export PATH=$PATH:$(pwd)/bin/
cd ..
# install openjdk
conda install -y -c bioconda/label/cf201901 java-jdk
# install FIJI
wget https://downloads.imagej.net/fiji/Life-Line/fiji-linux64-20170530.zip
unzip fiji-linux64-20170530.zip
mv ./Fiji.app/ ./fiji
cd ./fiji/jars && ln -s $(ls ij-1.*.jar) ij.jar
cd ../..
export PATH=$PATH:/fiji
mkdir -p ./fiji/data
# install plugins
cd ./fiji/plugins && wget -O imagescience.jar https://imagescience.org/meijering/software/download/imagescience.jar
wget -O FeatureJ_.jar https://imagescience.org/meijering/software/download/FeatureJ_.jar
wget https://github.com/ijpb/MorphoLibJ/releases/download/v1.3.6/MorphoLibJ_-1.3.6.jar
cd ../..
# get the imagej macro
wget https://raw.githubusercontent.com/Neubias-WG5/W_NucleiTracking-ImageJ/master/NucleiTracking.ijm
mv NucleiTracking.ijm ./fiji/macros/macro.ijm