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FROM ubuntu:20.04
ENV DEBIAN_FRONTEND=noninteractive
RUN apt-get update && apt-get upgrade -y
RUN apt install -y build-essential liblapack-dev libblas-dev gfortran autoconf automake cmake curl git libtool libcurl4-openssl-dev pkg-config unzip wget zlib1g-dev python3-dev python3-pip python3-venv python3-wheel
RUN apt-get install -y --no-install-recommends software-properties-common dirmngr
RUN wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
# add the R 4.0 repo from CRAN -- adjust 'focal' to 'groovy' or 'bionic' as needed
RUN add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
RUN apt-get update
RUN apt install -y --no-install-recommends r-base
RUN R -e "install.packages(c('changepoint', 'data.table', 'randomForest', 'smoother', 'caret', 'BiocManager'))" && \
R -e "BiocManager::install('rhdf5')"
RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
bash Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda && \
/opt/conda/bin/conda init
RUN /opt/conda/bin/conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/ && \
/opt/conda/bin/conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/ && \
/opt/conda/bin/conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/ && \
/opt/conda/bin/conda config --set show_channel_urls yes
RUN mkdir /DEMINERS-main/
COPY ./* /DEMINERS-main/
RUN R CMD INSTALL /DEMINERS-main/DecodeR_0.1.0.tar.gz
RUN cd /DEMINERS-main && \
/opt/conda/bin/conda create -y -n densecall python=3.9 seaborn=0.13.2 && . ~/.bashrc && \
conda activate /opt/conda/envs/densecall && \
pip install --upgrade pip && pip install -r requirements.txt -i https://mirrors.tuna.tsinghua.edu.cn/pypi/web/simple && \
python setup.py develop && cd ont-bonito-0.7.3 && \
python setup.py develop
RUN cd /
WORKDIR /DEMINERS
CMD ["/bin/bash"]