Configure ImmuneBuilder pipeline for WES execution

- Update container image to harbor.cluster.omic.ai/omic/immunebuilder:latest
- Update input/output paths to S3 (s3://omic/eureka/immunebuilder/)
- Remove local mount containerOptions (not needed in k8s)
- Update homepage to Gitea repo URL
- Clean history to remove large model weight blobs

Dockerfile

@@ -0,0 +1,94 @@
+FROM mambaorg/micromamba:1.5.8
+
+# Set environment variables
+ENV DEBIAN_FRONTEND=noninteractive
+ENV MAMBA_DOCKERFILE_ACTIVATE=1
+
+# Install system dependencies as root
+USER root
+RUN apt-get update -y && \
+    apt-get install -y --no-install-recommends \
+    wget \
+    git \
+    procps \
+    hmmer \
+    curl \
+    && rm -rf /var/lib/apt/lists/*
+
+# Switch back to micromamba user
+USER $MAMBA_USER
+
+# Create conda environment with all dependencies (CPU version for compatibility)
+RUN micromamba install -y -n base -c conda-forge -c bioconda -c pytorch \
+    python=3.10 \
+    pytorch \
+    cpuonly \
+    openmm \
+    pdbfixer \
+    anarci \
+    numpy \
+    "scipy>=1.6" \
+    "einops>=0.3" \
+    requests \
+    && micromamba clean --all --yes
+
+# Install ImmuneBuilder via pip
+RUN /opt/conda/bin/pip install --no-cache-dir ImmuneBuilder
+
+# Pre-download model weights to avoid rate limiting at runtime
+USER root
+
+# Create cache directory that ImmuneBuilder expects
+RUN mkdir -p /opt/immunebuilder_weights
+
+# Download antibody models
+RUN curl -L -o /opt/immunebuilder_weights/antibody_model_1 --retry 5 --retry-delay 30 \
+    "https://zenodo.org/record/7258553/files/antibody_model_1?download=1" && \
+    curl -L -o /opt/immunebuilder_weights/antibody_model_2 --retry 5 --retry-delay 30 \
+    "https://zenodo.org/record/7258553/files/antibody_model_2?download=1" && \
+    curl -L -o /opt/immunebuilder_weights/antibody_model_3 --retry 5 --retry-delay 30 \
+    "https://zenodo.org/record/7258553/files/antibody_model_3?download=1" && \
+    curl -L -o /opt/immunebuilder_weights/antibody_model_4 --retry 5 --retry-delay 30 \
+    "https://zenodo.org/record/7258553/files/antibody_model_4?download=1"
+
+# Download nanobody models
+RUN curl -L -o /opt/immunebuilder_weights/nanobody_model_1 --retry 5 --retry-delay 30 \
+    "https://zenodo.org/record/7258553/files/nanobody_model_1?download=1" && \
+    curl -L -o /opt/immunebuilder_weights/nanobody_model_2 --retry 5 --retry-delay 30 \
+    "https://zenodo.org/record/7258553/files/nanobody_model_2?download=1" && \
+    curl -L -o /opt/immunebuilder_weights/nanobody_model_3 --retry 5 --retry-delay 30 \
+    "https://zenodo.org/record/7258553/files/nanobody_model_3?download=1" && \
+    curl -L -o /opt/immunebuilder_weights/nanobody_model_4 --retry 5 --retry-delay 30 \
+    "https://zenodo.org/record/7258553/files/nanobody_model_4?download=1"
+
+# Download TCR models (TCRBuilder2+ weights)
+RUN curl -L -o /opt/immunebuilder_weights/tcr_model_1 --retry 5 --retry-delay 30 \
+    "https://zenodo.org/record/10581165/files/tcr_model_1?download=1" && \
+    curl -L -o /opt/immunebuilder_weights/tcr_model_2 --retry 5 --retry-delay 30 \
+    "https://zenodo.org/record/10581165/files/tcr_model_2?download=1" && \
+    curl -L -o /opt/immunebuilder_weights/tcr_model_3 --retry 5 --retry-delay 30 \
+    "https://zenodo.org/record/10581165/files/tcr_model_3?download=1" && \
+    curl -L -o /opt/immunebuilder_weights/tcr_model_4 --retry 5 --retry-delay 30 \
+    "https://zenodo.org/record/10581165/files/tcr_model_4?download=1"
+
+# Set permissions and create symlinks for all users
+RUN chmod -R 755 /opt/immunebuilder_weights && \
+    mkdir -p /root/.cache/ImmuneBuilder && \
+    ln -sf /opt/immunebuilder_weights/* /root/.cache/ImmuneBuilder/ && \
+    mkdir -p /home/$MAMBA_USER/.cache/ImmuneBuilder && \
+    ln -sf /opt/immunebuilder_weights/* /home/$MAMBA_USER/.cache/ImmuneBuilder/ && \
+    chown -R $MAMBA_USER:$MAMBA_USER /home/$MAMBA_USER/.cache
+
+# Create symlinks for the tools
+RUN ln -sf /opt/conda/bin/ABodyBuilder2 /usr/local/bin/abodybuilder2 && \
+    ln -sf /opt/conda/bin/NanoBodyBuilder2 /usr/local/bin/nanobodybuilder2 && \
+    ln -sf /opt/conda/bin/TCRBuilder2 /usr/local/bin/tcrbuilder2
+
+# Create working directory
+WORKDIR /workspace
+
+USER $MAMBA_USER
+
+# Set default entrypoint (micromamba entrypoint activates the environment)
+ENTRYPOINT ["/usr/local/bin/_entrypoint.sh"]
+CMD ["ABodyBuilder2", "--help"]