FROM rocker/r-ver:latest

RUN useradd --create-home --shell /bin/bash zim-gast 
RUN mkdir /home/zim-gast/rnaseq-workshop

LABEL org.opencontainers.image.licenses="GPL-2.0-or-later" \
      org.opencontainers.image.source="https://github.com/rocker-org/rocker-versioned2" \
      org.opencontainers.image.vendor="Rocker Project" \
      org.opencontainers.image.authors="Carl Boettiger <cboettig@ropensci.org>"

ENV S6_VERSION=v2.1.0.2
ENV RSTUDIO_VERSION=daily
ENV DEFAULT_USER=rstudio
ENV PANDOC_VERSION=default
ENV QUARTO_VERSION=default
ENV PATH=/usr/lib/rstudio-server/bin:$PATH

RUN /rocker_scripts/install_rstudio.sh
RUN /rocker_scripts/install_pandoc.sh
RUN /rocker_scripts/install_quarto.sh

RUN apt update
RUN apt upgrade -y
RUN apt install zlib1g-dev
RUN apt install libhdf5-dev -y

RUN Rscript -e "install.packages('ggplot2')"
RUN Rscript -e "install.packages('ggrepel')"
RUN Rscript -e "install.packages('gridExtra')"
RUN Rscript -e "if (!require('BiocManager', quietly = TRUE)){install.packages('BiocManager')}"
RUN Rscript -e "BiocManager::install('topGO')"
RUN Rscript -e "BiocManager::install('Rgraphviz')"
RUN Rscript -e "BiocManager::install('AnnotationDbi')"
RUN Rscript -e "BiocManager::install('rhdf5')"
RUN Rscript -e "install.packages('devtools')"
RUN Rscript -e "devtools::install_github('pachterlab/sleuth')"


EXPOSE 8787
WORKDIR /home/zim-gast/rnaseq-workshop

#CMD ["bash"]
CMD ["/init"]
