Dockerfile

#Dockerfile for jupyter-rethomics
FROM jupyterhub/jupyterhub

# pre-requisites
RUN apt-get update && \
    apt-get install -y --no-install-recommends fonts-dejavu apt-utils nano jq git gfortran file gcc cmake libcurl4-openssl-dev \
    libfontconfig1-dev libharfbuzz-dev libfribidi-dev libtiff-dev wget && \
    apt-get clean && \
    rm -rf /var/lib/apt/lists/*

# R - add cran repo for last R version
RUN apt-get update && \
    apt-get install -y lsb-release software-properties-common dirmngr && \
    apt-get clean && \
    rm -rf /var/lib/apt/lists/*

#get key
RUN wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
RUN add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/" -y

# Install R from Cran REPO
RUN apt-get update && \
    apt-get install -y libxml2-dev r-base r-base-dev && \
    rm -rf /var/lib/apt/lists/*

#install jupyter lab
RUN apt-get update && \
    apt-get install -y jupyter && \
    rm -rf /var/lib/apt/lists/*

#Will install version 3.6.4
RUN pip3 install jupyterlab --ignore-installed

#To upgrade to version 4.0.2
#RUN pip3 install jupyterlab --upgrade

#Jupyter extensions
#This is compatible only with 3.*
RUN pip3 install jupyterlab-spreadsheet-editor


# Install Ethoscope and related packages
RUN pip3 install pandas seaborn bokeh lifelines
RUN pip3 install opencv-python mysql-connector
RUN cd /opt/ && \
    git clone https://github.com/gilestrolab/ethoscope.git && \
    cd ethoscope && git checkout dev && \
    cd src && python3 setup.py develop 

#add the default user ethoscolab with password ethoscolab
RUN useradd -m ethoscopelab
RUN echo 'ethoscopelab:ethoscopelab' | chpasswd

#install ethoscopy
#https://github.com/Lblackhurst29/ethoscopy
RUN pip3 install ethoscopy pycatch22

#install R packages and rethomics
COPY install_r_packages.r /root/install_r_packages.r
RUN ln -s /bin/tar /bin/gtar && \
    Rscript /root/install_r_packages.r

#activate the multiuser jupyterlab in hub
COPY jupyterhub_config.py /srv/jupyterhub/jupyterhub_config.py

WORKDIR /srv/jupyterhub/

EXPOSE 8000

LABEL maintainer="Giorgio Gilestro <giorgio@gilest.ro>"
LABEL org.jupyter.service="ethoscope-lab"

CMD ["sh", "-c", "jupyterhub"]