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b8a800e | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 | FROM python:3.9-slim
# Install system dependencies
RUN apt-get update && apt-get install -y \
wget \
curl \
build-essential \
gcc \
g++ \
make \
libffi-dev \
libssl-dev \
libglib2.0-0 \
libxext6 \
libsm6 \
libxrender1 \
libgomp1 \
&& rm -rf /var/lib/apt/lists/*
# Install Miniforge (conda-forge–based; no Anaconda ToS) and configure channels
RUN wget -q https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh && \
bash Miniforge3-Linux-x86_64.sh -b -p /opt/conda && \
rm Miniforge3-Linux-x86_64.sh
ENV PATH="/opt/conda/bin:${PATH}"
# Add bioconda; conda-forge is default for Miniforge. No Anaconda ToS needed.
RUN conda config --add channels bioconda && \
conda config --set channel_priority flexible
# Install mamba for faster package installation
RUN conda install -n base -c conda-forge mamba -y
# Install AMBER tools, PyMOL, AutoDock Vina 1.1.2, Open Babel, RDKit, and gemmi (for Meeko)
RUN mamba install -y python=3.11 \
conda-forge::ambertools conda-forge::pymol-open-source \
bioconda::autodock-vina conda-forge::openbabel conda-forge::rdkit conda-forge::gemmi
# Clean up conda/mamba cache to reduce image size
RUN conda clean -afy
# Install Python packages via pip (only packages not provided by conda or that need pip)
# Note: numpy, pandas, matplotlib are already installed by conda; don't override to avoid conflicts
RUN pip install --no-cache-dir \
flask==2.3.3 \
flask-cors==4.0.0 \
biopython \
seaborn \
mdanalysis \
gunicorn==21.2.0 \
requests \
meeko>=0.7.0 \
prody \
"numpy<2.0"
# Set working directory
WORKDIR /AmberMDFlow
# Copy the entire project
COPY . .
# Create necessary directories with proper permissions
RUN mkdir -p /AmberMDFlow/obsolete /AmberMDFlow/pdb /AmberMDFlow/temp /AmberMDFlow/output && \
chmod -R 777 /AmberMDFlow
# Make sure the ambermdflow package is on the Python path
ENV PYTHONPATH="${PYTHONPATH}:/AmberMDFlow"
# Expose the port
EXPOSE 7860
# Run the application
CMD ["python", "start_web_server.py"]
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