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# Get R, Rstudio, python, in ubuntu image based on rocker-version2
FROM bioconductor/bioconductor_docker:RELEASE_3_16
ENV PATH $PATH:/opt/conda/bin
RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh && \
/bin/bash ~/miniconda.sh -b -p /opt/conda && \
rm ~/miniconda.sh && \
ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc
COPY scraps_conda.yml .
RUN /opt/conda/bin/conda config --add channels defaults && \
/opt/conda/bin/conda config --add channels bioconda && \
/opt/conda/bin/conda config --add channels conda-forge && \
conda install -c conda-forge mamba && \
mamba env update -n base -f scraps_conda.yml && \
conda clean -afy
RUN R -e 'BiocManager::install("rnabioco/scrapR")'
WORKDIR /home/rstudio