57 lines
3.0 KiB
Plaintext
57 lines
3.0 KiB
Plaintext
# Use Ubuntu 22.04 as base image
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FROM ubuntu:22.04
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LABEL maintainer="lingyu zeng <pylyzeng@gmail.com>"
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ENV TZ=Asia/Shanghai
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ENV DEBIAN_FRONTEND=noninteractive
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# $(curl https://ipapi.co/timezone)
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# Configure timezone and install necessary packages
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RUN sed -i 's/archive.ubuntu.com/mirrors.aliyun.com/g' /etc/apt/sources.list && \
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sed -i 's/security.ubuntu.com/mirrors.aliyun.com/g' /etc/apt/sources.list && \
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apt-get update && \
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ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone && \
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apt-get install -y tzdata && \
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apt-get install -y git zip curl wget bzip2 libgl1-mesa-glx g++ sudo software-properties-common && \
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adduser --disabled-password --gecos "" developer && \
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echo "developer ALL=(ALL) NOPASSWD: ALL" > /etc/sudoers.d/developer && \
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sudo apt-get autoremove -y && \
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apt-get clean && \
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rm -rf /var/lib/apt/lists/*
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# Set environment variables
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ENV PATH="/home/developer/bin:/home/developer/micromamba/bin:${PATH}"
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ENV CONDA_PREFIX="/home/developer/micromamba/envs/pyrosetta"
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# Switch to user developer
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USER developer
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# Set working directory
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WORKDIR /home/developer
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# Copy necessary files to the working directory
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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/
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# Update and install necessary packages
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RUN unzip EvoEF2-master.zip && \
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chmod +x EvoEF2-master/build.sh && \
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cd EvoEF2-master && \
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./build.sh && \
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cd .. && \
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tar zxvf _foldxLinux64.tar_.gz && \
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chmod +x install_scwrl4.0.2_64bit_2020_linux && \
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echo -e "Y\nLicense Holder Name" | ./install_scwrl4.0.2_64bit_2020_linux ./ && \
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# Install Micromamba
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wget -qO- https://micromamba.snakepit.net/api/micromamba/linux-64/latest | tar -xvj bin/micromamba && \
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./bin/micromamba shell init --shell bash --root-prefix=~/micromamba && \
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mkdir -p ~/noarch && mkdir ~/work && sudo chmod -R 777 ~/work && \
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mv repodata.json ~/noarch && \
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mv pyrosetta-2023.31+release.1799523-py311_0.tar.bz2 ~/noarch && \
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./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 && \
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rm -rf EvoEF2-master.zip install_scwrl4.0.2_64bit_2020_linux _foldxLinux64.tar_.gz ~/noarch
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WORKDIR /home/developer/work
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VOLUME ["/home/developer/work"]
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ENTRYPOINT ["/home/developer/micromamba/envs/pyrosetta/bin/python", "/home/developer/mutation.py"]
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# 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）
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# PermissionError: [Errno 13] Permission denied: '/home/developer/work/4i24.clean.pdb'
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# 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
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# 映射宿主机的目录/home/zenglingyu/tools/dockertest权限要求是777，否则会报错 |