ddhmed/prodigal repository overview

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# https://pyrodigal.readthedocs.io/en/stable/api/gene_finder.html#pyrodigal.GeneFinder
# sudo docker build -t ddhmed/prodigal:2.6.3 .
# sudo docker run -it --rm -v $PWD:/work -p 8000:8000 ddhmed/prodigal:2.6.3
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# 使用基础镜像
FROM ubuntu:latest

### 作者和邮箱
MAINTAINER ddhmed [email protected]

USER root

# 设置时区，避免交互式提示
ENV TZ=Asia/Shanghai
RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone

# 安装基本工具和Python
RUN apt-get update && apt-get install -y \
    build-essential \
    cmake \
    git \
    curl \
    wget \
    ca-certificates \
    libjpeg-dev \
    libpng-dev \
    python3 \
    python3-dev \
    python3-pip \
    && rm -rf /var/lib/apt/lists/*

# 创建一个符号链接，使 python3 命令可以用 python 调用
RUN ln -s /usr/bin/python3 /usr/bin/python

# 升级pip
#RUN pip3 install --upgrade pip

# install base packages
RUN pip install --no-cache-dir --break-system-packages \
    numpy \
    scipy \
    pandas \
    scikit-learn \
    matplotlib \
    jupyterlab

# This will install the prodigal binary in /usr/local/bin. 
#RUN git clone https://github.com/hyattpd/Prodigal.git && \
#    cd Prodigal &&\
#    make install
RUN pip install --no-cache-dir --break-system-packages pyrodigal biopython scikit-bio

# 清理不必要的文件
RUN apt-get clean && \
    rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

### 设置工作目录
WORKDIR /work

# 暴露 Jupyter Notebook 端口
EXPOSE 8000

CMD ["jupyter", "lab", "--allow-root", "--ip=0.0.0.0", "--port=8000"]