FROM renku/renkulab-r:4.0.3-0.10.3
USER root

RUN apt-get update && \
    apt-get install -y --no-install-recommends \
    apt-utils \
    dirmngr \
    gpg-agent \
    less \
    libcurl4-openssl-dev \
    libxml2-dev \
    libz-dev \
    software-properties-common

USER ${NB_USER}

# install the R dependencies
COPY install.R /tmp/
RUN R -f /tmp/install.R

# install the python dependencies
COPY requirements.txt environment.yml /tmp/
RUN conda env update -q -f /tmp/environment.yml && \
    /opt/conda/bin/pip install --ignore-installed -r /tmp/requirements.txt && \
    conda clean -y --all && \
    conda env export -n "root"

# install our utilities package

COPY --chown=rstudio:rstudio src /code/src
RUN ln -s /code/src && \
    mkdir -p ~/.local/bin

RUN pip install -e src/covid-19/covid_19_utils

RUN wget -O ~/.local/bin/jq https://github.com/stedolan/jq/releases/download/jq-1.6/jq-linux64 && \
    chmod u+x ~/.local/bin/jq