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FROM node:14 as jsbuild | ||
ENV REPO=https://github.com/MetaCell/NetPyNE-UI.git | ||
ENV BRANCH_TAG=release/1.0.0 | ||
ENV FOLDER=netpyne | ||
RUN echo "no-cache 2023-7-14" | ||
RUN git clone $REPO -b $BRANCH_TAG $FOLDER | ||
RUN rm -Rf .git | ||
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COPY overrides/geppetto/GeppettoConfiguration.json $FOLDER/webapp/GeppettoConfiguration.json | ||
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WORKDIR $FOLDER/webapp | ||
RUN yarn install --network-timeout 1000000000 | ||
RUN yarn build-dev | ||
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RUN rm -Rf node_modules/* | ||
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### | ||
FROM jupyter/base-notebook:hub-1.4.2 | ||
ENV NB_UID=jovyan | ||
ENV FOLDER=netpyne | ||
ENV NP_LFPYKIT_HEAD_FILE=/home/jovyan/nyhead.mat | ||
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USER root | ||
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RUN rm -rf /var/lib/apt/lists | ||
RUN apt-get update -qq &&\ | ||
apt-get install python3-tk vim nano unzip git make libtool g++ -qq pkg-config libfreetype6-dev libpng-dev libopenmpi-dev -y | ||
RUN apt-get install openjdk-11-jre-headless -y | ||
RUN conda install python=3.7 -y | ||
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WORKDIR $FOLDER | ||
COPY --from=jsbuild --chown=1000:1000 $FOLDER/requirements.txt requirements.txt | ||
RUN --mount=type=cache,target=/root/.cache python -m pip install --upgrade pip &&\ | ||
pip install -r requirements.txt --prefer-binary | ||
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COPY --from=jsbuild --chown=1000:1000 $FOLDER . | ||
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# ToDo: fixme, for now remove the jupyter hub config json file because it overrides the default | ||
# and thus removes the frame ancestor cors settings | ||
RUN rm -f ~/.jupyter/*.json | ||
RUN chown $NB_UID . | ||
RUN chown $NB_UID /opt | ||
RUN rm -Rf workspace | ||
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USER $NB_UID | ||
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# sym link workspace pvc to $FOLDER | ||
RUN mkdir -p /opt/workspace | ||
RUN mkdir -p /opt/user | ||
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ENV NEURON_HOME=/opt/conda | ||
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USER root | ||
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RUN jupyter nbextension install --py --symlink --sys-prefix jupyter_geppetto | ||
RUN jupyter nbextension enable --py --sys-prefix jupyter_geppetto | ||
RUN jupyter nbextension enable --py --sys-prefix widgetsnbextension | ||
RUN jupyter serverextension enable --py --sys-prefix jupyter_geppetto | ||
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RUN --mount=type=cache,target=/root/.cache python -m pip install --upgrade pip &&\ | ||
python utilities/install.py --npm-skip --no-test | ||
FROM gcr.io/metacellllc/netpyne-ui:1.0.0-osb | ||
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COPY overrides/requirements.txt overrides/requirements.txt | ||
RUN --mount=type=cache,target=/root/.cache python -m pip install --upgrade pip &&\ | ||
pip install -r overrides/requirements.txt | ||
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RUN mv workspace /opt/workspace/tutorials | ||
RUN chown -R $NB_UID /opt/workspace/tutorials | ||
RUN ln -s /opt/workspace workspace | ||
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RUN jupyter labextension disable @jupyterlab/hub-extension | ||
RUN wget --no-check-certificate -O $NP_LFPYKIT_HEAD_FILE https://www.parralab.org/nyhead/sa_nyhead.mat | ||
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USER $NB_UID | ||
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EXPOSE 8888 | ||
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ENTRYPOINT ["tini", "-g", "--"] | ||
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CMD ./NetPyNE-UI |
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applications/netpyne/overrides/geppetto/GeppettoConfiguration.json
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