Add LigandMPNN Nextflow pipeline for protein sequence design

Dockerfile

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+FROM nvidia/cuda:12.1.0-cudnn8-runtime-ubuntu22.04
+
+# Set environment variables
+ENV DEBIAN_FRONTEND=noninteractive
+ENV PYTHONUNBUFFERED=1
+ENV PYTHONDONTWRITEBYTECODE=1
+
+# Set working directory
+WORKDIR /app
+
+# Install system dependencies including build tools for ProDy compilation
+RUN apt-get update -y && \
+    apt-get install -y --no-install-recommends \
+    wget \
+    git \
+    curl \
+    ca-certificates \
+    python3.11 \
+    python3.11-venv \
+    python3.11-dev \
+    python3-pip \
+    procps \
+    build-essential \
+    && rm -rf /var/lib/apt/lists/* \
+    && update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.11 1 \
+    && update-alternatives --install /usr/bin/python python /usr/bin/python3.11 1
+
+# Upgrade pip
+RUN python3 -m pip install --no-cache-dir --upgrade pip setuptools wheel
+
+# Clone LigandMPNN repository
+RUN git clone https://github.com/dauparas/LigandMPNN.git /app/LigandMPNN
+
+# Set working directory to LigandMPNN
+WORKDIR /app/LigandMPNN
+
+# Install Python dependencies
+RUN pip3 install --no-cache-dir \
+    biopython==1.79 \
+    filelock==3.13.1 \
+    fsspec==2024.3.1 \
+    Jinja2==3.1.3 \
+    MarkupSafe==2.1.5 \
+    mpmath==1.3.0 \
+    networkx==3.2.1 \
+    numpy==1.23.5 \
+    ProDy==2.4.1 \
+    pyparsing==3.1.1 \
+    scipy==1.12.0 \
+    sympy==1.12 \
+    typing_extensions==4.10.0 \
+    ml-collections==0.1.1 \
+    dm-tree==0.1.8
+
+# Install PyTorch with CUDA support
+RUN pip3 install --no-cache-dir \
+    torch==2.2.1 \
+    --index-url https://download.pytorch.org/whl/cu121
+
+# Download model parameters
+RUN mkdir -p /app/LigandMPNN/model_params && \
+    wget -q https://files.ipd.uw.edu/pub/ligandmpnn/proteinmpnn_v_48_002.pt -O /app/LigandMPNN/model_params/proteinmpnn_v_48_002.pt && \
+    wget -q https://files.ipd.uw.edu/pub/ligandmpnn/proteinmpnn_v_48_010.pt -O /app/LigandMPNN/model_params/proteinmpnn_v_48_010.pt && \
+    wget -q https://files.ipd.uw.edu/pub/ligandmpnn/proteinmpnn_v_48_020.pt -O /app/LigandMPNN/model_params/proteinmpnn_v_48_020.pt && \
+    wget -q https://files.ipd.uw.edu/pub/ligandmpnn/proteinmpnn_v_48_030.pt -O /app/LigandMPNN/model_params/proteinmpnn_v_48_030.pt && \
+    wget -q https://files.ipd.uw.edu/pub/ligandmpnn/ligandmpnn_v_32_005_25.pt -O /app/LigandMPNN/model_params/ligandmpnn_v_32_005_25.pt && \
+    wget -q https://files.ipd.uw.edu/pub/ligandmpnn/ligandmpnn_v_32_010_25.pt -O /app/LigandMPNN/model_params/ligandmpnn_v_32_010_25.pt && \
+    wget -q https://files.ipd.uw.edu/pub/ligandmpnn/ligandmpnn_v_32_020_25.pt -O /app/LigandMPNN/model_params/ligandmpnn_v_32_020_25.pt && \
+    wget -q https://files.ipd.uw.edu/pub/ligandmpnn/ligandmpnn_v_32_030_25.pt -O /app/LigandMPNN/model_params/ligandmpnn_v_32_030_25.pt && \
+    wget -q https://files.ipd.uw.edu/pub/ligandmpnn/solublempnn_v_48_002.pt -O /app/LigandMPNN/model_params/solublempnn_v_48_002.pt && \
+    wget -q https://files.ipd.uw.edu/pub/ligandmpnn/solublempnn_v_48_010.pt -O /app/LigandMPNN/model_params/solublempnn_v_48_010.pt && \
+    wget -q https://files.ipd.uw.edu/pub/ligandmpnn/solublempnn_v_48_020.pt -O /app/LigandMPNN/model_params/solublempnn_v_48_020.pt && \
+    wget -q https://files.ipd.uw.edu/pub/ligandmpnn/solublempnn_v_48_030.pt -O /app/LigandMPNN/model_params/solublempnn_v_48_030.pt && \
+    wget -q https://files.ipd.uw.edu/pub/ligandmpnn/per_residue_label_membrane_mpnn_v_48_020.pt -O /app/LigandMPNN/model_params/per_residue_label_membrane_mpnn_v_48_020.pt && \
+    wget -q https://files.ipd.uw.edu/pub/ligandmpnn/global_label_membrane_mpnn_v_48_020.pt -O /app/LigandMPNN/model_params/global_label_membrane_mpnn_v_48_020.pt && \
+    wget -q https://files.ipd.uw.edu/pub/ligandmpnn/ligandmpnn_sc_v_32_002_16.pt -O /app/LigandMPNN/model_params/ligandmpnn_sc_v_32_002_16.pt && \
+    ls -la /app/LigandMPNN/model_params/
+
+# Create wrapper script for ligandmpnn (using absolute path)
+RUN printf '#!/bin/bash\npython /app/LigandMPNN/run.py "$@"\n' > /usr/local/bin/ligandmpnn && \
+    chmod +x /usr/local/bin/ligandmpnn
+
+# Create wrapper script for scoring (using absolute path)
+RUN printf '#!/bin/bash\npython /app/LigandMPNN/score.py "$@"\n' > /usr/local/bin/ligandmpnn-score && \
+    chmod +x /usr/local/bin/ligandmpnn-score
+
+# Create input/output directories
+RUN mkdir -p /app/inputs /app/outputs
+
+# Set environment variables for model paths
+ENV LIGANDMPNN_MODEL_DIR=/app/LigandMPNN/model_params
+ENV PYTHONPATH=/app/LigandMPNN:${PYTHONPATH:-}
+
+WORKDIR /app/LigandMPNN
+
+CMD ["python", "run.py", "--help"]