Dockerfile

FROM nvidia/cuda:12.6.0-base-ubuntu22.04

# Install Python, Node.js, miniconda, dependencies
RUN apt-get update && apt-get install -y \
    python3.10 \
    python3.10-distutils \
    python3.10-venv \
    python3.10-dev \
    python3-pip \
    bash \
    net-tools \
    iputils-ping \
    curl \
    git \
    wget \
    nano \
    gfortran \
    && apt-get clean && rm -rf /var/lib/apt/lists/*

# Upgrade pip to the latest version
RUN curl -sS https://bootstrap.pypa.io/get-pip.py | python3.10 \
    && python3.10 -m pip install --upgrade pip
RUN python3.10 --version

# Install Conda
RUN curl -sLo /miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh \
    && bash /miniconda.sh -b -p /miniconda \
    && rm /miniconda.sh
ENV PATH="/miniconda/bin:${PATH}"

RUN curl -fsSL https://deb.nodesource.com/setup_20.x | bash - && \
    apt-get install -y nodejs

# Set the working directory
WORKDIR /app

# Set LIB
ARG LIB

# Copy the backend application
COPY requirements.txt    /app/requirements.txt
COPY src/LICENSE    /app/src/LICENSE
COPY src/Git2APP /app/src/Git2APP
COPY src/R2APP    /app/src/R2APP
COPY src/configs    /app/src/configs
COPY src/dataloader    /app/src/dataloader
COPY src/deploy    /app/src/deploy
COPY src/gpt    /app/src/gpt
COPY src/inference    /app/src/inference
COPY src/models    /app/src/models
COPY src/prompt    /app/src/prompt
COPY src/report    /app/src/report
COPY src/scripts    /app/src/scripts
COPY src/retrievers    /app/src/retrievers
COPY images    /app/images
#COPY src/tmp    /app/src/tmp
COPY data/standard_process/scanpy/ /app/data/standard_process/scanpy/
COPY data/standard_process/squidpy/ /app/data/standard_process/squidpy/
COPY data/standard_process/ehrapy/ /app/data/standard_process/ehrapy/
COPY data/standard_process/snapatac2/ /app/data/standard_process/snapatac2/
COPY data/standard_process/base/ /app/data/standard_process/base/
COPY data/autocoop/scanpy/ /app/data/autocoop/scanpy/
COPY data/autocoop/squidpy/ /app/data/autocoop/squidpy/
COPY data/autocoop/ehrapy/ /app/data/autocoop/ehrapy/
COPY data/autocoop/snapatac2/ /app/data/autocoop/snapatac2/
COPY data/conversations/ /app/data/conversations/
COPY data/others-data/ /app/data/others-data/
COPY hugging_models/retriever_model_finetuned/scanpy/ /app/hugging_models/retriever_model_finetuned/scanpy/
COPY hugging_models/retriever_model_finetuned/squidpy/ /app/hugging_models/retriever_model_finetuned/squidpy/
COPY hugging_models/retriever_model_finetuned/ehrapy/ /app/hugging_models/retriever_model_finetuned/ehrapy/
COPY hugging_models/retriever_model_finetuned/snapatac2/ /app/hugging_models/retriever_model_finetuned/snapatac2/
COPY docker_utils/ /app/docker_utils/

# mkdir tmp
RUN mkdir -p /app/src/tmp

# Install Python dependencies
RUN python3.10 -m pip install --no-cache-dir -r /app/requirements.txt --verbose

# Install dependencies from environment.yml if it exists
RUN if [ -f /app/docker_utils/${LIB}/environment.yml ]; then \
        conda env create -f /app/docker_utils/${LIB}/environment.yml; \
    fi

# Install dependencies from requirements.sh if it exists
RUN if [ -f /app/docker_utils/${LIB}/requirements.sh ]; then \
        chmod +x /app/docker_utils/${LIB}/requirements.sh && \
        /app/docker_utils/${LIB}/requirements.sh; \
    fi

COPY chatbot_ui_biomania/ /app/chatbot_ui_biomania/

# Install node modules and build the front-end
# RUN cd /app/chatbot_ui_biomania && npm install && npm run build
RUN cd /app/chatbot_ui_biomania && \
    npm install react-markdown@7.0.0 rehype-raw@6.0.0 \
    npm install && \
    npm run build

# run the start script
RUN chmod +x /app/docker_utils/${LIB}/docker_start_script.sh

# Set environment variables
ENV CUDA_VISIBLE_DEVICES=0
ENV PYTHONPATH="/app:${PYTHONPATH}"
ENV BACKEND_URL="http://localhost:5000"

# Expose ports
EXPOSE 3000

# Start command
CMD /app/docker_utils/${LIB}/docker_start_script.sh