Initial commit: Chai-1 protein structure prediction pipeline for WES

- Nextflow pipeline using chai1 Docker image from Harbor
- S3-based input/output paths (s3://omic/eureka/chai-lab/)
- GPU-accelerated protein folding with MSA support

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Dockerfile

@@ -0,0 +1,56 @@
+# Use NVIDIA CUDA base image with Ubuntu 22.04
+FROM nvidia/cuda:12.1.0-cudnn8-devel-ubuntu22.04
+
+# Set environment variables
+ENV DEBIAN_FRONTEND=noninteractive \
+    LANG=C.UTF-8 \
+    LC_ALL=C.UTF-8 \
+    PYTHONUNBUFFERED=TRUE \
+    PYTHONFAULTHANDLER=1 \
+    PYTHONPYCACHEPREFIX='/tmp/.chai_pycache' \
+    MYPY_CACHE_DIR='/tmp/.chai_mypy_cache'
+
+# Install system dependencies
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    git \
+    wget \
+    curl \
+    ca-certificates \
+    python3.10 \
+    python3.10-dev \
+    python3-pip \
+    build-essential \
+    && rm -rf /var/lib/apt/lists/*
+
+# Set working directory
+WORKDIR /workspace
+
+# Upgrade pip
+RUN pip3 install --no-cache-dir --upgrade pip setuptools wheel
+
+# Install chai_lab first (this will install older PyTorch)
+RUN pip3 install --no-cache-dir chai_lab==0.5.2
+
+# Force uninstall old PyTorch and related packages
+RUN pip3 uninstall -y torch torchvision torchaudio
+
+# Install PyTorch 2.6+ from main PyPI (has CUDA support built-in)
+RUN pip3 install --no-cache-dir torch torchvision torchaudio
+
+# Upgrade transformers to ensure compatibility
+RUN pip3 install --no-cache-dir --upgrade "transformers>=4.30.0"
+
+# Verify all installations
+RUN python3 -c "import torch; v=torch.__version__.split('+')[0]; print(f'PyTorch: {v}'); major,minor=map(int,v.split('.')[:2]); assert (major==2 and minor>=6) or major>2, f'PyTorch {v} is too old, need 2.6+'" && \
+    python3 -c "import torch; print(f'CUDA available: {torch.cuda.is_available()}')" && \
+    python3 -c "from transformers import EsmModel; print('transformers: OK')" && \
+    python3 -c "import typer; print('typer: OK')" && \
+    python3 -c "import chai_lab; print('chai_lab: OK')" && \
+    chai --help
+
+# Add entry point script
+COPY entrypoint.sh /workspace/
+RUN chmod +x /workspace/entrypoint.sh
+
+# Set entry point
+ENTRYPOINT ["/workspace/entrypoint.sh"]