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.chailab

@@ -0,0 +1,83 @@
+FROM ubuntu:22.04 AS chailab-baseimage
+
+ENV \
+  LANG=C.UTF-8 \
+  LC_ALL=C.UTF-8 \
+  # config for apt
+  DEBIAN_FRONTEND=noninteractive \
+  # default editor for git cli
+  EDITOR=vim \
+  # keep (large) mypy cache outside of working tree
+  MYPY_CACHE_DIR='/tmp/.chai_lab_mypy_cache' \
+  # always flush output from python
+  PYTHONUNBUFFERED=TRUE \
+  # enable fault handler (print tracebacks even after segfault or NCCL errors).
+  PYTHONFAULTHANDLER=1 \
+  # keep __pycache__ out of working tree
+  PYTHONPYCACHEPREFIX='/tmp/.chai_lab_pycache'
+
+
+RUN --mount=type=cache,target=/var/cache/apt \
+  apt-get -qq update \
+  && apt-get -qq install -y \
+  # common things
+  gnupg ca-certificates wget git curl aria2 lsb-release tzdata \
+  rsync sudo tree htop tmux unzip \
+  clang \
+  # for direct ssh into container
+  openssh-server socat \
+  # provides `fuser` command
+  psmisc \
+  # RDMA/InfiniBand
+  libibverbs1 librdmacm1 \
+  # text editors, needed by git cli
+  nano vim \
+  build-essential libstdc++6 \
+  # python
+  python3.10 python3.10-dev \
+  # (run continues)
+  # stop git from complaining about dubious ownership.
+  && git config --global --add safe.directory "*" \
+  #
+  # cuda softlinking is needed in podman, but not docker
+  && ln -s /lib/x86_64-linux-gnu/libcuda.so.1 /lib/x86_64-linux-gnu/libcuda.so \
+  && ldconfig /lib/x86_64-linux-gnu/ \
+  # setup timezone, to $TZ, ubuntu-specific
+  # && ln -fs /usr/share/zoneinfo/$TZ /etc/localtime \
+  && dpkg-reconfigure --frontend noninteractive tzdata \
+  # change default shell to bash (has no effect during building)
+  && chsh -s /bin/bash
+
+
+ENV \
+  # expose CUDA libraries. Now that we don't build anything this is likely redundant
+  LD_LIBRARY_PATH="/usr/local/cuda/lib64/stubs/:${LD_LIBRARY_PATH:-}" \
+  # Set uv timeout to larger value to account for slow download time of nvidia-cudnn-cu12
+  UV_HTTP_TIMEOUT=1000 \
+  # where virtual env will be installed
+  VIRTUAL_ENV=/opt/venv
+
+# Install dependencies in virtualenv
+COPY ./requirements.in /tmp/requirements.in
+# from https://pythonspeed.com/articles/activate-virtualenv-dockerfile/
+# a trick to have virtualenv "always activated"
+ENV PATH="$VIRTUAL_ENV/bin:$PATH"
+
+RUN --mount=type=cache,target=/root/.cache/uv \
+  # Install uv
+  curl -LsSf https://astral.sh/uv/0.5.4/install.sh | sh \
+  && . $HOME/.local/bin/env \
+  && uv venv --no-python-downloads $VIRTUAL_ENV \
+  # this is sh, not bash, so . not source
+  && . $VIRTUAL_ENV/bin/activate \
+  && uv pip install uv pip -r /tmp/requirements.in
+
+
+# making sure envvars are set in all shells
+RUN echo "PATH=\"$PATH\"" >> /etc/environment \
+  && echo "LANG=\"$LANG\"" >> /etc/environment \
+  && echo "LC_ALL=\"$LC_ALL\"" >> /etc/environment \
+  && echo "LD_LIBRARY_PATH=\"$LD_LIBRARY_PATH\"" >> /etc/environment \
+  && echo "EDITOR=\"$EDITOR\"" >> /etc/environment
+
+# no startup command.