Dockerfile

FROM renku/renkulab-r:4.0.0-renku0.10.4-0.6.3
# see https://github.com/SwissDataScienceCenter/renkulab-docker
# to swap this image for the latest version available

# Uncomment and adapt if code is to be included in the image
# COPY src /code/src

# Uncomment and adapt if your R or python packages require extra linux (ubuntu) software
# e.g. the following installs apt-utils and vim; each pkg on its own line, all lines
# except for the last end with backslash '\' to continue the RUN line
#
USER root
RUN apt-get update && \
    /opt/conda/bin/python3 -m pip install --upgrade pip && \
    apt-get install -y --no-install-recommends && \
    conda update --all -y
#    apt-utils \
#    vim
USER ${NB_USER}

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

# install the python dependencies
COPY requirements.txt /tmp/
COPY environment.yml /tmp/
RUN pip3 install -r /tmp/requirements.txt
RUN conda env update -n base --file /tmp/environment.yml

USER root
RUN conda update --all -y
USER ${NB_USER}