dockerfile

# Use the Ubuntu 20.04 image of NVIDIA CUDA 11.7.1 and cuDNN as the base image
FROM nvidia/cuda:11.7.1-devel-ubuntu20.04

ENV DEBIAN_FRONTEND=noninteractive

# Install necessary packages
RUN apt-get update && apt-get install -y \
    libxrender1 \
    wget \
    g++ \
    cmake \
    zip \
    curl \
    ca-certificates \
    git \
    && rm -rf /var/lib/apt/lists/*

# isntall Miniconda
RUN wget -q https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O /tmp/miniconda.sh \
    && bash /tmp/miniconda.sh -b -p /root/miniconda3 \
    && rm /tmp/miniconda.sh

# init Miniconda and create conda env
ENV PATH="/root/miniconda3/bin:$PATH"
RUN conda init bash \
    && . /root/.bashrc \
    && conda create -n OpenBioMed python=3.9 -y \
    && conda activate OpenBioMed \
    && pip install --upgrade pip setuptools

# Installing PyTorch and torchvision (using conda run to install in OpenBioMed env)
RUN conda run -n OpenBioMed pip install torch==1.13.1+cu117 torchvision==0.14.1+cu117 torchaudio==0.13.1 --extra-index-url https://download.pytorch.org/whl/cu117 \
    && conda run -n OpenBioMed pip install pyg_lib torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-1.13.1+cu117.html \
    && conda run -n OpenBioMed pip install pytorch_lightning==2.0.8 peft==0.9.0 accelerate==1.3.0 --no-deps

# Set working directory and copy application files
WORKDIR /app
COPY . /app/

# Install additional packages from requirements.txt
RUN conda run -n OpenBioMed pip install -r requirements.txt

# Install visualization tools
RUN conda install -n OpenBioMed -c conda-forge pymol-open-source -y \
    && conda run -n OpenBioMed pip install imageio

# Install AutoDockVina tools (proxy removed - use Docker build args if needed)
RUN conda run -n OpenBioMed pip install meeko==0.1.dev3 pdb2pqr vina==1.2.2 \
    && conda run -n OpenBioMed pip install git+https://github.com/Valdes-Tresanco-MS/AutoDockTools_py3

# Install NLTK
RUN conda run -n OpenBioMed pip install spacy rouge_score nltk \
    && conda run -n OpenBioMed python -c "import nltk; nltk.download('wordnet'); nltk.download('omw-1.4')"

# Activate the OpenBioMed environment by default
RUN echo "source activate OpenBioMed" >> ~/.bashrc
ENV PATH="/root/miniconda3/envs/OpenBioMed/bin:$PATH"

# Make entrypoint executable
RUN chmod +x ./scripts/run_server.sh || true

# Set default command
ENTRYPOINT ["./scripts/run_server.sh"]