# Use Ubuntu 22.04 as base image
FROM ubuntu:22.04
LABEL maintainer="lingyu zeng <pylyzeng@gmail.com>"
ENV TZ=Asia/Shanghai
ENV DEBIAN_FRONTEND=noninteractive
# $(curl https://ipapi.co/timezone)
# Configure timezone and install necessary packages  
RUN sed -i 's/archive.ubuntu.com/mirrors.aliyun.com/g' /etc/apt/sources.list && \
    sed -i 's/security.ubuntu.com/mirrors.aliyun.com/g' /etc/apt/sources.list && \
    apt-get update && \
    ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone && \
    apt-get install -y tzdata && \
    apt-get install -y git zip curl wget bzip2 libgl1-mesa-glx g++ sudo software-properties-common && \
    adduser --disabled-password --gecos "" developer && \
    echo "developer ALL=(ALL) NOPASSWD: ALL" > /etc/sudoers.d/developer && \
    sudo apt-get autoremove -y && \
    apt-get clean && \
    rm -rf /var/lib/apt/lists/*

# Set environment variables
ENV PATH="/home/developer/bin:/home/developer/micromamba/bin:${PATH}"
ENV CONDA_PREFIX="/home/developer/micromamba/envs/pyrosetta"

# Switch to user developer
USER developer

# Set working directory
WORKDIR /home/developer

# Copy necessary files to the working directory
COPY --chown=developer .condarc mutation.py 4i24.pdb test.list _foldxLinux64.tar_.gz EvoEF2-master.zip install_scwrl4.0.2_64bit_2020_linux pyrosetta-2023.31+release.1799523-py311_0.tar.bz2 noarch/repodata.json .condarc /home/developer/

# Update and install necessary packages
RUN unzip EvoEF2-master.zip && \
    chmod +x EvoEF2-master/build.sh && \
    cd EvoEF2-master && \
    ./build.sh && \
    cd .. && \
    tar zxvf _foldxLinux64.tar_.gz && \
    chmod +x install_scwrl4.0.2_64bit_2020_linux && \
    echo -e "Y\nLicense Holder Name" | ./install_scwrl4.0.2_64bit_2020_linux ./ && \
    # Install Micromamba
    wget -qO- https://micromamba.snakepit.net/api/micromamba/linux-64/latest | tar -xvj bin/micromamba && \
    ./bin/micromamba shell init --shell bash --root-prefix=~/micromamba && \
    mkdir -p ~/noarch && mkdir ~/work && sudo chmod -R 777 ~/work && \
	mv repodata.json ~/noarch && \
    mv pyrosetta-2023.31+release.1799523-py311_0.tar.bz2 ~/noarch && \
    ./bin/micromamba create -n pyrosetta -c conda-forge -c bioconda -c defaults python=3.11 click loguru biopython pymol-open-source pyrosetta-2023.31+release.1799523-py311_0.tar.bz2 -y && \
    rm -rf EvoEF2-master.zip install_scwrl4.0.2_64bit_2020_linux _foldxLinux64.tar_.gz ~/noarch

WORKDIR /home/developer/work
VOLUME ["/home/developer/work"]
ENTRYPOINT ["/home/developer/micromamba/envs/pyrosetta/bin/python", "/home/developer/mutation.py"]
# 普通用户使用的版本总有奇怪的权限问题（待解决），可以考虑使用Dockerfile构建root用户的镜像（通过测试）
# PermissionError: [Errno 13] Permission denied: '/home/developer/work/4i24.clean.pdb'
# docker run --rm -it -v /home/zenglingyu/tools/dockertest:/home/developer/work hotwa/test1:latest rosetta -p /home/developer/work/4i24.pdb -m /home/developer/work/test.list
# 映射宿主机的目录/home/zenglingyu/tools/dockertest权限要求是777，否则会报错