FROM dceoy/r-tidyverse

MAINTAINER Kiran V Garimella

# install some utilities
RUN apt-get update -m
RUN apt-get install -y wget datamash bsdmainutils git-lfs bzip2 ca-certificates libglib2.0-0 libxext6 libsm6 libxrender1 git mercurial subversion

# install conda
RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O /miniconda.sh \
        && bash /miniconda.sh -b -p /miniconda
ENV PATH=/miniconda/bin/:/miniconda/envs/metrics/bin/:/root/google-cloud-sdk/bin/:${PATH}

# install conda packages
COPY ./environment.yml /
RUN conda env create -f /environment.yml && conda clean -a
RUN echo "source activate metrics" > ~/.bashrc
RUN activate metrics

# install more R packages
#RUN set -e \
#    && clir update \
#    && clir install --devt=cran vroom \
#    && clir validate vroom

# install gatk
RUN git clone https://github.com/broadinstitute/gatk.git -b kvg_pbeap \
    && cd gatk \
    && ./gradlew \
    && cp /gatk/build/libs/gatk-package-4.1.0.0-54-g47086b6-SNAPSHOT-local.jar /usr/local/bin/gatk.jar \
    && cd .. \
    && rm -rf /gatk

# install picard
RUN wget -O /picard.jar https://github.com/broadinstitute/picard/releases/download/2.22.1/picard.jar

# remove the entry point that we inherited from the r-tidyverse docker
ENTRYPOINT []
WORKDIR /
CMD ["/bin/bash"]
