--- a +++ b/docker/Dockerfile @@ -0,0 +1,35 @@ +FROM ubuntu:18.04 +ENV SHELL=/bin/bash +RUN apt-get update && apt-get install -y git curl +RUN apt-get install -y python3-setuptools python3-dev build-essential python3-pip && apt-get clean +RUN apt-get install -y libsm6 libxext6 libxrender-dev openslide-tools && apt-get clean + +RUN pip3 install cython numpy pandas jupyter +#RUN pip3 install git+https://github.com/DSLituiev/slideslicer +ARG CACHEBUST=2 +RUN git clone https://github.com/dslituiev/slideslicer +RUN cd slideslicer/ && pip3 install . + +### DOWNLOAD FILES +RUN mkdir data + +COPY 14112.* data/ +#RUN fileid="1-s87PeyZY2C6ZejCyn4Cy0iYEkTeEFrP" &&\ +# filename=data/14112.svs &&\ +# curl -c ./cookie -s -L "https://drive.google.com/uc?export=download&id=${fileid}" > /dev/null &&\ +# curl -Lb ./cookie "https://drive.google.com/uc?export=download&confirm=`awk '/download/ {print $NF}' ./cookie`&id=${fileid}" -o ${filename} &&\ +# rm cookie +# +#RUN fileid="1JRBfyzeyMdg0WTc2McC_wOiYrXhi4iRx" &&\ +# filename=data/14112.xml &&\ +# curl -c ./cookie -s -L "https://drive.google.com/uc?export=download&id=${fileid}" > /dev/null && \ +# curl -Lb ./cookie "https://drive.google.com/uc?export=download&confirm=`awk '/download/ {print $NF}' ./cookie`&id=${fileid}" -o ${filename} &&\ +# rm cookie +COPY resnet50_mouse_gloms_scale4.h5 data/ + +RUN ln -s /data slideslicer +RUN pip3 install scikit-learn tensorflow keras +CMD mkdir -p slideslicer/notebooks + +CMD cd slideslicer/notebooks && jupyter-notebook --port 8899 --ip=0.0.0.0 --allow-root +