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