update

Dockerfile_developer

@@ -0,0 +1,57 @@
+# 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