Dockerfile.jupyter

FROM jupyter/datascience-notebook:72cca2a7f3ea

USER root

RUN apt-get update \
    && apt-get install -y --no-install-recommends zip \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/*

USER jovyan

RUN pip2 install --upgrade pip
RUN pip3 install --upgrade pip

# Install Python 2 & 3 Additional Packages for Notebooks
ADD requirements.txt requirements.txt
RUN pip2 install -r requirements.txt 
RUN pip3 install -r requirements.txt 

# Install R Packages used in Treehouse
RUN conda config --system --add channels conda-forge
RUN conda config --system --add channels defaults
RUN conda config --system --add channels r
RUN conda config --system --add channels bioconda
RUN conda install --yes -c r r-data.table=1.10.0 r-xml=3.98_1.5
RUN conda clean -tipsy

RUN R -e "install.packages(c('reshape2', 'openxlsx'), repos='http://cran.rstudio.com/')"

RUN Rscript -e 'source("http://bioconductor.org/biocLite.R"); biocLite("biomaRt")'
RUN Rscript -e 'source("http://bioconductor.org/biocLite.R"); biocLite("pathview")'

# Run as root so we can access everything under /data
USER root