Dockerfile

FROM jupyter/minimal-notebook
LABEL Author="Sylvain Soliman <Sylvain.Soliman@inria.fr>"
LABEL Maintainer="Biocham team <biocham@inria.fr>"

USER root

ENV LD_LIBRARY_PATH /usr/local/lib/
ENV PYTHONPATH /home/$NB_USER/biocham/
ENV PATH /home/$NB_USER/biocham:$PATH
RUN cd /home/$NB_USER/ && \
	wget https://lifeware.gitlabpages.inria.fr/biocham/biocham.zip && \
	unzip biocham.zip && rm biocham.zip
RUN cd biocham && ./install.sh && apt-get autoremove -y && \
	apt-get clean -y && rm -rf /var/lib/apt/lists/*
RUN conda uninstall -y --force terminado
RUN chown -R $NB_USER:users /home/$NB_USER/ && chmod -R 755 /home/$NB_USER/.local
# WTF permission error
RUN mv /home/$NB_USER/.local /tmp/ && mv /tmp/.local /home/$NB_USER/
RUN mv /home/$NB_USER/biocham /tmp/ && mv /tmp/biocham /home/$NB_USER/

USER $NB_USER
RUN ln -s /home/$NB_USER/biocham/library/examples /home/$NB_USER/work/

CMD ["start.sh", "biocham", "--notebook"]