Dockerfile for the st spot detector

Dockerfile

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+# HOW TO:
+#
+# First build this image with:
+#    docker build -t spot_detector:latest ./
+#
+# Then to start the container running the server run:
+#    docker run -d -p 8080:8080 --name spotdetector_deamon -i spot_detector:latest
+#
+# For an interactive session run:
+#    docker run -p 8080:8080 --name spotdetector -ti spot_detector:latest bash
+# Then within the container run:
+#     cd /opt/repos/st_spot_detector/server && python -m app
+#
+# FINALLY: use chrome/firefox or something to go to http://0.0.0.0:8080
+# also feel free to run with wsgi instead if you think thats fun
+
+FROM ubuntu:18.04
+
+ENV DEBIAN_FRONTEND noninteractive
+RUN apt-get update
+RUN apt-get install apt-utils --yes
+RUN apt-get upgrade --yes
+RUN apt-get install -y tzdata
+RUN apt-get install -y build-essential \
+                       cmake \
+                       git \
+                       wget \
+                       curl \
+                       zlib1g-dev \
+                       libbz2-dev \
+                       liblzma-dev \
+                       libopencv-dev \
+                       pkg-config \
+                       libjpeg8-dev \
+                       libtiff5-dev \
+                       libavcodec-dev \
+                       libavformat-dev \
+                       libswscale-dev \
+                       libv4l-dev \
+                       libxvidcore-dev \
+                       libx264-dev \
+                       libgtk-3-dev \
+                       libatlas-base-dev \
+                       gfortran \
+                       curl \
+                       libboost-all-dev
+
+# get nodejs 10
+WORKDIR /opt/
+RUN curl -sL https://deb.nodesource.com/setup_10.x | bash -
+RUN apt-get install -y nodejs
+
+# install python and packages
+RUN apt-get install -y python3-pip python3-dev python3-tk \
+  && cd /usr/local/bin \
+  && ln -s /usr/bin/python3 python \
+  && pip3 install --upgrade pip
+RUN pip install --upgrade pip
+RUN pip install numpy
+RUN pip install setuptools
+
+# make a dir or the repos
+RUN mkdir /opt/repos
+
+# setup and install st_tissue_recognition
+WORKDIR /opt/repos
+RUN git clone https://github.com/SpatialTranscriptomicsResearch/st_tissue_recognition.git
+WORKDIR /opt/repos/st_tissue_recognition
+RUN mkdir /opt/repos/st_tissue_recognition/build
+WORKDIR /opt/repos/st_tissue_recognition/build
+RUN cmake ../
+RUN make install
+WORKDIR /opt/repos/st_tissue_recognition/python-module/
+RUN python setup.py install
+RUN echo "export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH" >> $HOME/.bashrc
+
+# setup the st spot detector
+WORKDIR /opt/repos
+RUN git clone https://github.com/SpatialTranscriptomicsResearch/st_spot_detector.git
+WORKDIR /opt/repos/st_spot_detector
+RUN pip install -r server/requirements.txt
+RUN pip install websockets==5.0
+WORKDIR /opt/repos/st_spot_detector/client
+RUN npm install
+RUN make dist 
+
+# set ldlibrarypath, port and start command
+ENV LD_LIBRARY_PATH /usr/local/lib:$LD_LIBRARY_PATH
+EXPOSE 8080
+WORKDIR /opt/repos/st_spot_detector/server
+CMD ["python","-m","app"]
+
+COPY Dockerfile /opt