Dockerfile

FROM condaforge/miniforge3:24.11.3-0

WORKDIR /app

ENV DEBIAN_FRONTEND=noninteractive
ENV PATH=/opt/conda/bin:$PATH
ENV LD_LIBRARY_PATH=/opt/conda/envs/ailixir/lib:/opt/conda/envs/dp/lib:/opt/conda/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu

SHELL ["/bin/bash", "-lc"]

RUN apt-get update && apt-get install -y --no-install-recommends \
    git \
    wget \
    curl \
    ca-certificates \
    build-essential \
    make \
    procps \
    ocl-icd-opencl-dev \
    pocl-opencl-icd \
    clinfo \
    && rm -rf /var/lib/apt/lists/*

# -----------------------------
# Generation / REINVENT env
# -----------------------------
RUN conda create -n ailixir python=3.10 -y && conda clean -afy

SHELL ["conda", "run", "--no-capture-output", "-n", "ailixir", "/bin/bash", "-lc"]

RUN set -eux; \
    for i in 1 2 3 4 5; do \
      if conda install -y -c conda-forge \
        pandas \
        numpy \
        scikit-learn \
        rdkit \
        fastapi \
        uvicorn \
        requests \
        tqdm \
        pip; then \
        conda clean -afy; \
        exit 0; \
      fi; \
      echo "conda install failed on attempt ${i}, retrying..."; \
      conda clean -i -y || true; \
      sleep $((i * 20)); \
    done; \
    echo "conda install failed after retries"; \
    exit 1

RUN git clone --depth 1 https://github.com/MolecularAI/REINVENT4.git /opt/REINVENT4 \
    && cd /opt/REINVENT4 \
    && python install.py cpu

RUN python -c "from rdkit import Chem; print('RDKit import OK')"
RUN python -c "import importlib.metadata as m; print('REINVENT version', m.version('reinvent'))"

# Meeko provides mk_prepare_ligand.py for PDBQT ligand preparation used by docking
# Install with required runtime dependencies because pip meeko may not pull all of them.
RUN set -eux; \
    for i in 1 2 3 4 5; do \
      if conda install -y -c conda-forge meeko gemmi scipy; then \
        conda clean -afy; \
        which mk_prepare_ligand.py; \
        mk_prepare_ligand.py -h >/tmp/mk_prepare_ligand_help.txt; \
        exit 0; \
      fi; \
      echo "meeko install failed on attempt ${i}, retrying..."; \
      conda clean -i -y || true; \
      sleep $((i * 20)); \
    done; \
    echo "meeko install failed after retries"; \
    exit 1

# Open Babel provides obabel for MOL2 ligand export
RUN set -eux; \
    for i in 1 2 3 4 5; do \
      if conda install -y -c conda-forge openbabel; then \
        conda clean -afy; \
        which obabel; \
        obabel -V; \
        exit 0; \
      fi; \
      echo "openbabel install failed on attempt ${i}, retrying..."; \
      conda clean -i -y || true; \
      sleep $((i * 20)); \
    done; \
    echo "openbabel install failed after retries"; \
    exit 1


# -----------------------------
# DeepPurpose affinity env
# -----------------------------
SHELL ["/bin/bash", "-lc"]

RUN conda create -n dp python=3.8 -y && conda clean -afy

SHELL ["conda", "run", "--no-capture-output", "-n", "dp", "/bin/bash", "-lc"]

RUN set -eux; \
    for i in 1 2 3 4 5; do \
      if conda install -y -c conda-forge \
        pandas \
        numpy \
        scikit-learn \
        rdkit \
        fastapi \
        uvicorn \
        requests \
        tqdm \
        pip; then \
        conda clean -afy; \
        exit 0; \
      fi; \
      echo "conda install failed on attempt ${i}, retrying..."; \
      conda clean -i -y || true; \
      sleep $((i * 20)); \
    done; \
    echo "conda install failed after retries"; \
    exit 1

ENV PIP_DEFAULT_TIMEOUT=1000
ENV PIP_RETRIES=10
ENV PIP_DISABLE_PIP_VERSION_CHECK=1

RUN pip install --no-cache-dir --default-timeout=1000 --retries=10 \
    git+https://github.com/bp-kelley/descriptastorus

RUN pip install --no-cache-dir --default-timeout=1000 --retries=10 \
    torch==2.1.0 \
    --index-url https://download.pytorch.org/whl/cpu

RUN python -c "import torch; print('Torch version:', torch.__version__); print('CUDA available:', torch.cuda.is_available())"

RUN pip install --no-cache-dir --default-timeout=1000 --retries=10 \
    DeepPurpose

# -----------------------------
# AutoDock-GPU CPU/OpenCL build
# -----------------------------
SHELL ["/bin/bash", "-lc"]

RUN set -eux; \
    clinfo || true; \
    rm -rf /opt/AutoDock-GPU; \
    git clone --depth 1 https://github.com/ccsb-scripps/AutoDock-GPU.git /opt/AutoDock-GPU; \
    cd /opt/AutoDock-GPU; \
    make DEVICE=CPU NUMWI=1 GPU_INCLUDE_PATH=/usr/include GPU_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu; \
    find /opt/AutoDock-GPU -maxdepth 3 -type f -name "autodock_*" -print; \
    test -f /opt/AutoDock-GPU/bin/autodock_cpu_1wi; \
    chmod +x /opt/AutoDock-GPU/bin/autodock_cpu_1wi

COPY api.py /app/api.py
COPY bundle /app/bundle
COPY start_hf.sh /app/start_hf.sh

RUN sed -i 's/\r$//' /app/start_hf.sh \
    && chmod +x /app/start_hf.sh \
    && mkdir -p /app/outputs/jobs /app/outputs/deeppurpose \
    && mkdir -p /home/abdullah/projects/egfr_drug_discovery/runs/deeppurpose


ENV PUBLIC_BASE_URL=http://localhost:7860
ENV REINVENT_DEVICE=cpu
ENV DEEPPURPOSE_URL=http://127.0.0.1:8001/reinvent_predict
ENV ADGPU_BIN=/opt/AutoDock-GPU/bin/autodock_cpu_1wi
ENV PYTHON=python
ENV LD_PRELOAD=/opt/conda/envs/ailixir/lib/libstdc++.so.6
ENV PYTHONPATH=/app/bundle

EXPOSE 7860

CMD ["/app/start_hf.sh"]