FROM docker.io/rocker/r-ver:4.4.1
RUN apt-get update -qq && apt-get install -y -qq \
    ncbi-blast+ \
    && rm -rf /var/cache/apt/* /var/lib/apt/lists/*

RUN /rocker_scripts/install_tidyverse.sh
RUN apt-get update && apt-get install -y \
      libglpk-dev \
    && rm -rf /var/cache/apt/* /var/lib/apt/lists/*;
RUN install2.r --error --skipinstalled --ncpus -1 \
        optparse \
        BiocManager \
    && Rscript -e 'BiocManager::install(c("Biostrings","GenomicRanges"))' \
    && rm -rf /tmp/downloaded_packages

ENV FATOOLS_DIR="/app"
COPY db/ /app/db
COPY bin/ /app/bin

VOLUME /cwd
WORKDIR /cwd
ENV PATH=$PATH:/app/bin
ENTRYPOINT []
