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from python:3.7-buster
ENV DEBIAN_FRONTEND=noninteractive
RUN mkdir -p /usr/share/man/man1 /usr/share/man/man2
RUN apt-get update && \
apt-get install -y --no-install-recommends \
openjdk-11-jre
# Prints installed java version, just for checking
RUN java --version
# ---------------------------------------------------------------------------------------------------------------------
# Install Cytomine python client
RUN git clone https://github.com/cytomine-uliege/Cytomine-python-client.git && \
cd /Cytomine-python-client && git checkout tags/v2.7.3 && pip install . && \
rm -r /Cytomine-python-client
# ---------------------------------------------------------------------------------------------------------------------
# Fiji installation
# Install virtual X server
RUN apt-get update && apt-get install -y unzip xvfb libx11-dev libxtst-dev libxrender-dev
# Install Fiji.
RUN wget https://downloads.imagej.net/fiji/Life-Line/fiji-linux64-20170530.zip
RUN unzip fiji-linux64-20170530.zip
RUN mv Fiji.app/ fiji
# create a sym-link with the name jars/ij.jar that is pointing to the current version jars/ij-1.nm.jar
RUN cd /fiji/jars && ln -s $(ls ij-1.*.jar) ij.jar
# Add fiji to the PATH
ENV PATH $PATH:/fiji
RUN mkdir -p /fiji/data
# Clean up
RUN rm fiji-linux64-20170530.zip
# ---------------------------------------------------------------------------------------------------------------------
# Install BIAFLOWS (annotation exporter, compute metrics, helpers,...)
RUN apt-get update && apt-get install libgeos-dev -y && apt-get clean
RUN git clone https://github.com/Neubias-WG5/biaflows-utilities.git && \
cd /biaflows-utilities/ && git checkout tags/v0.9.1 && pip install .
# install utilities binaries
RUN chmod +x /biaflows-utilities/bin/*
RUN cp /biaflows-utilities/bin/* /usr/bin/
# cleaning
RUN rm -r /biaflows-utilities
# ---------------------------------------------------------------------------------------------------------------------
# Install Fiji plugins
RUN cd /fiji/plugins && wget -O MorphoLibJ_-1.3.6.jar https://github.com/ijpb/MorphoLibJ/releases/download/v1.3.6/MorphoLibJ_-1.3.6.jar
RUN cd /fiji/plugins && wget -O imagescience.jar http://www.imagescience.org/meijering/software/download/imagescience.jar
RUN cd /fiji/plugins && wget -O mcib3d-core-4.1.5.jar https://mcib3d.frama.io/3d-suite-imagej/uploads/mcib3d-core-4.1.5.jar
RUN cd /fiji/plugins && wget -O mcib3d_plugins-4.1.5.jar https://mcib3d.frama.io/3d-suite-imagej/uploads/mcib3d_plugins-4.1.5.jar
# ---------------------------------------------------------------------------------------------------------------------
# Install Macro
ADD IJNuclei3DSegmentation.ijm /fiji/macros/macro.ijm
ADD wrapper.py /app/wrapper.py
# for running the wrapper locally
ADD descriptor.json /app/descriptor.json
ENTRYPOINT ["python", "/app/wrapper.py"]