| FROM docker.io/ubuntu:22.04 |
|
|
| ENV TZ=Asia/Shanghai |
| ENV R_REMOTE_ERR=1 |
| ENV DEBIAN_FRONTEND=noninteractive |
|
|
| RUN apt-get update -y && \ |
| apt-get install -y --no-install-recommends \ |
| build-essential \ |
| software-properties-common \ |
| dirmngr \ |
| wget \ |
| unzip \ |
| make \ |
| lsb-release && \ |
| rm -rf /var/lib/apt/lists/* |
|
|
|
|
| RUN apt-get update -y \ |
| && apt-get -y install iputils-ping \ |
| && apt-get -y install wget \ |
| && apt-get -y install net-tools \ |
| && apt-get -y install vim \ |
| && apt-get -y install openssh-server \ |
| && apt-get -y install python3.9 \ |
| && apt-get -y install python3-pip \ |
| && apt-get -y install git \ |
| && cd /usr/local/bin \ |
| && rm -f python \ |
| && rm -f python3 \ |
| && rm -f pip \ |
| && rm -f pip3 \ |
| && ln -s /usr/bin/python3.9 python \ |
| && ln -s /usr/bin/python3.9 python3 \ |
| && ln -s /usr/bin/pip3 pip \ |
| && ln -s /usr/bin/pip3 pip3 \ |
| && apt-get clean |
| RUN apt install -y libpcre2-dev libdeflate-dev liblzma-dev libbz2-dev libblas-dev gfortran libicu-dev liblapack-dev libxml2-dev |
| RUN apt install --no-install-recommends software-properties-common dirmngr |
| RUN wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc |
| RUN add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/" |
| RUN apt install --no-install-recommends r-base -y |
| RUN R -e "install.packages('remotes', repos = 'https://cloud.r-project.org/'); \ |
| remotes::install_version('ape', version = '5.8.1', dependencies = TRUE, repos = 'https://cloud.r-project.org/'); \ |
| remotes::install_version('igraph', version = '2.1.4', dependencies = TRUE, repos = 'https://cloud.r-project.org/'); \ |
| remotes::install_version('openxlsx', version = '4.2.8', dependencies = TRUE, repos = 'https://cloud.r-project.org/')" && \ |
| rm -rf /tmp/Rtmp* |
| |
| RUN useradd -m -u 1000 user |
| USER user |
| ENV PATH="/home/user/.local/bin:$PATH" |
| WORKDIR /app |
| RUN git clone https://github.com/pylelab/USalign.git |
| WORKDIR /app/USalign |
| RUN make |
| WORKDIR /app |
| RUN chmod -R 777 /app |
| COPY --chmod=777 ./requirements.txt requirements.txt |
| RUN pip install --no-cache-dir --upgrade -r requirements.txt |
| RUN pip install rpy2==3.2.0 |
| RUN pip install pandas==1.5.3 |
| RUN pip install numpy==1.25.0 |
| RUN pip install gradio==5.44.1 |
| COPY --chmod=777 . /app |
| ENV MPLCONFIGDIR="/home/user/.config/matplotlib" |
| CMD ["python3", "app.py"] |
