FROM ubuntu:16.04

MAINTAINER xufeng <crazyhsu9527@gmail.com>

# install basic dependencies

RUN sed -i s@/archive.ubuntu.com/@/mirrors.tuna.tsinghua.edu.cn/@g /etc/apt/sources.list && \

    apt-get clean && apt-get update && apt-get install -y --no-install-recommends \

    build-essential \

    cmake \

    git \

    wget \

    apt-transport-https \

    libz-dev \

    ca-certificates \

    vim \

    less \

    sudo \

    apt-utils \

    libgfortran3 \

    openjdk-8-jdk

RUN wget --no-check-certificate https://mirrors.tuna.tsinghua.edu.cn/anaconda/miniconda/Miniconda3-latest-Linux-x86_64.sh -O /root/miniconda3.sh && \

    /bin/bash /root/miniconda3.sh -b -p /root/conda && \

    rm /root/miniconda3.sh

ENV PATH=/root/conda/bin:$PATH

RUN conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/ && \

    conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/ && \

    conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/ && \

    conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/ && \

    conda update --all -y && conda create -n modas python=3.8 -y

ENV CONDA_DEFAULT_ENV=modas

ENV CONDA_PREFIX=/root/conda/envs/$CONDA_DEFAULT_ENV

ENV CONDA_AUTO_UPDATE_CONDA=false

RUN echo ". /root/conda/etc/profile.d/conda.sh" >> ~/.bashrc && \

    echo "conda activate modas" >> ~/.bashrc

RUN mkdir /root/.pip && echo "[global]\nindex-url = https://pypi.tuna.tsinghua.edu.cn/simple" > /root/.pip/pip.conf && \

    $CONDA_PREFIX/bin/pip install MODAS && \

    conda install -y -c conda-forge r-rcppeigen r=3.6 rpy2 && \

    conda install -y -c anaconda gcc_linux-64 gxx_linux-64 gfortran_linux-64