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Marco Lenoir
MarcoTheBlack/
deepvariant
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# Copyright 2019 Google LLC.





  
  

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# This is used to build the DeepSomatic release docker image.





  
  

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# It can also be used to build local images, especially if you've made changes





  
  

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# to the code.





  
  

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# Example command:





  
  

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# $ git clone https://github.com/google/deepvariant.git





  
  

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# $ cd deepvariant





  
  

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# $ sudo docker build -f Dockerfile.deepsomatic -t deepsomatic .





  
  

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#





  
  

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# To build for GPU, use a command like:





  
  

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# $ sudo docker build -f Dockerfile.deepsomatic --build-arg=FROM_IMAGE=nvidia/cuda:11.8.0-cudnn8-devel-ubuntu22.04 --build-arg=DV_GPU_BUILD=1 -t deepsomatic_gpu .





  
  

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ARG FROM_IMAGE=ubuntu:22.04





  
  

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# PYTHON_VERSION is also set in settings.sh.





  
  

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ARG PYTHON_VERSION=3.10





  
  

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ARG DV_GPU_BUILD=0





  
  

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ARG VERSION_DEEPSOMATIC=1.8.0





  
  

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ARG TF_ENABLE_ONEDNN_OPTS=1





  
  

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FROM continuumio/miniconda3 as conda_setup





  
  

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RUN conda config --add channels defaults && \





  
  

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    conda config --add channels bioconda && \





  
  

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    conda config --add channels conda-forge





  
  

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RUN conda create -n bio \





  
  

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                    bioconda::bcftools=1.15 \





  
  

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                    bioconda::samtools=1.15 \





  
  

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    && conda clean -a





  
  

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FROM ${FROM_IMAGE} as builder





  
  

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COPY --from=conda_setup /opt/conda /opt/conda





  
  

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LABEL maintainer="https://github.com/google/deepvariant/issues"





  
  

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ARG DV_GPU_BUILD





  
  

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ENV DV_GPU_BUILD=${DV_GPU_BUILD}





  
  

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# Copying DeepVariant source code





  
  

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COPY . /opt/deepvariant





  
  

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WORKDIR /opt/deepvariant





  
  

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RUN ./build-prereq.sh \





  
  

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  && PATH="${HOME}/bin:${PATH}" ./build_release_binaries.sh  # PATH for bazel





  
  

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FROM ${FROM_IMAGE}





  
  

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ARG DV_GPU_BUILD





  
  

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ARG VERSION_DEEPSOMATIC





  
  

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ARG PYTHON_VERSION





  
  

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ARG TF_ENABLE_ONEDNN_OPTS





  
  

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ENV DV_GPU_BUILD=${DV_GPU_BUILD}





  
  

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ENV VERSION_DEEPSOMATIC ${VERSION_DEEPSOMATIC}





  
  

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ENV PYTHON_VERSION ${PYTHON_VERSION}





  
  

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ENV TF_ENABLE_ONEDNN_OPTS ${TF_ENABLE_ONEDNN_OPTS}





  
  

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WORKDIR /opt/





  
  

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COPY --from=builder /opt/deepvariant/bazel-bin/licenses.zip .





  
  

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WORKDIR /opt/deepvariant/bin/





  
  

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COPY --from=builder /opt/conda /opt/conda





  
  

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COPY --from=builder /opt/deepvariant/run-prereq.sh .





  
  

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COPY --from=builder /opt/deepvariant/settings.sh .





  
  

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COPY --from=builder /opt/deepvariant/bazel-out/k8-opt/bin/deepvariant/make_examples_somatic.zip  .





  
  

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COPY --from=builder /opt/deepvariant/bazel-out/k8-opt/bin/deepvariant/call_variants.zip  .





  
  

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COPY --from=builder /opt/deepvariant/bazel-out/k8-opt/bin/deepvariant/postprocess_variants.zip  .





  
  

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COPY --from=builder /opt/deepvariant/bazel-out/k8-opt/bin/deepvariant/vcf_stats_report.zip  .





  
  

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COPY --from=builder /opt/deepvariant/bazel-out/k8-opt/bin/deepvariant/show_examples.zip  .





  
  

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COPY --from=builder /opt/deepvariant/bazel-out/k8-opt/bin/deepvariant/runtime_by_region_vis.zip  .





  
  

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COPY --from=builder /opt/deepvariant/scripts/run_deepsomatic.py ./deepsomatic/





  
  

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RUN ./run-prereq.sh





  
  

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RUN update-alternatives --install /usr/bin/python3 python3 /usr/bin/python${PYTHON_VERSION} 0 && \





  
  

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    update-alternatives --install /usr/bin/python python /usr/bin/python${PYTHON_VERSION} 0





  
  

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# Create shell wrappers for python zip files for easier use.





  
  

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RUN \





  
  

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  BASH_HEADER='#!/bin/bash' && \





  
  

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  printf "%s\n%s\n" \





  
  

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    "${BASH_HEADER}" \





  
  

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    'python3 -u /opt/deepvariant/bin/make_examples_somatic.zip "$@"' > \





  
  

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    /opt/deepvariant/bin/make_examples_somatic && \





  
  

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  printf "%s\n%s\n" \





  
  

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    "${BASH_HEADER}" \





  
  

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    'python3 /opt/deepvariant/bin/call_variants.zip "$@"' > \





  
  

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    /opt/deepvariant/bin/call_variants && \





  
  

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  printf "%s\n%s\n" \





  
  

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    "${BASH_HEADER}" \





  
  

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    'python3 /opt/deepvariant/bin/postprocess_variants.zip "$@"' > \





  
  

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    /opt/deepvariant/bin/postprocess_variants && \





  
  

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  printf "%s\n%s\n" \





  
  

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    "${BASH_HEADER}" \





  
  

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    'python3 /opt/deepvariant/bin/vcf_stats_report.zip "$@"' > \





  
  

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    /opt/deepvariant/bin/vcf_stats_report && \





  
  

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  printf "%s\n%s\n" \





  
  

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    "${BASH_HEADER}" \





  
  

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    'python3 /opt/deepvariant/bin/show_examples.zip "$@"' > \





  
  

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    /opt/deepvariant/bin/show_examples && \





  
  

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  printf "%s\n%s\n" \





  
  

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    "${BASH_HEADER}" \





  
  

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    'python3 /opt/deepvariant/bin/runtime_by_region_vis.zip "$@"' > \





  
  

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    /opt/deepvariant/bin/runtime_by_region_vis && \





  
  

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  printf "%s\n%s\n" \





  
  

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    "${BASH_HEADER}" \





  
  

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    'python3 -u /opt/deepvariant/bin/deepsomatic/run_deepsomatic.py "$@"' > \





  
  

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    /opt/deepvariant/bin/deepsomatic/run_deepsomatic && \





  
  

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  chmod +x /opt/deepvariant/bin/make_examples_somatic \





  
  

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    /opt/deepvariant/bin/call_variants \





  
  

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    /opt/deepvariant/bin/postprocess_variants \





  
  

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    /opt/deepvariant/bin/vcf_stats_report \





  
  

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    /opt/deepvariant/bin/show_examples \





  
  

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    /opt/deepvariant/bin/runtime_by_region_vis \





  
  

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    /opt/deepvariant/bin/deepsomatic/run_deepsomatic





  
  

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# Copy models





  
  

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WORKDIR /opt/models/deepsomatic/wgs





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepSomatic/${VERSION_DEEPSOMATIC}/savedmodels/deepsomatic.wgs.savedmodel/fingerprint.pb .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepSomatic/${VERSION_DEEPSOMATIC}/savedmodels/deepsomatic.wgs.savedmodel/saved_model.pb .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepSomatic/${VERSION_DEEPSOMATIC}/savedmodels/deepsomatic.wgs.savedmodel/example_info.json .





  
  

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WORKDIR /opt/models/deepsomatic/wgs/variables





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepSomatic/${VERSION_DEEPSOMATIC}/savedmodels/deepsomatic.wgs.savedmodel/variables/variables.data-00000-of-00001 .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepSomatic/${VERSION_DEEPSOMATIC}/savedmodels/deepsomatic.wgs.savedmodel/variables/variables.index .





  
  

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RUN chmod -R +r /opt/models/deepsomatic/wgs/*





  
  

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WORKDIR /opt/models/deepsomatic/wes





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepSomatic/${VERSION_DEEPSOMATIC}/savedmodels/deepsomatic.wes.savedmodel/fingerprint.pb .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepSomatic/${VERSION_DEEPSOMATIC}/savedmodels/deepsomatic.wes.savedmodel/saved_model.pb .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepSomatic/${VERSION_DEEPSOMATIC}/savedmodels/deepsomatic.wes.savedmodel/example_info.json .





  
  

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WORKDIR /opt/models/deepsomatic/wes/variables





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepSomatic/${VERSION_DEEPSOMATIC}/savedmodels/deepsomatic.wes.savedmodel/variables/variables.data-00000-of-00001 .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepSomatic/${VERSION_DEEPSOMATIC}/savedmodels/deepsomatic.wes.savedmodel/variables/variables.index .





  
  

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RUN chmod -R +r /opt/models/deepsomatic/wes/*





  
  

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WORKDIR /opt/models/deepsomatic/pacbio





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepSomatic/${VERSION_DEEPSOMATIC}/savedmodels/deepsomatic.pacbio.savedmodel/fingerprint.pb .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepSomatic/${VERSION_DEEPSOMATIC}/savedmodels/deepsomatic.pacbio.savedmodel/saved_model.pb .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepSomatic/${VERSION_DEEPSOMATIC}/savedmodels/deepsomatic.pacbio.savedmodel/example_info.json .





  
  

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WORKDIR /opt/models/deepsomatic/pacbio/variables





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepSomatic/${VERSION_DEEPSOMATIC}/savedmodels/deepsomatic.pacbio.savedmodel/variables/variables.data-00000-of-00001 .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepSomatic/${VERSION_DEEPSOMATIC}/savedmodels/deepsomatic.pacbio.savedmodel/variables/variables.index .





  
  

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RUN chmod -R +r /opt/models/deepsomatic/pacbio/*





  
  

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WORKDIR /opt/models/deepsomatic/ont





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepSomatic/${VERSION_DEEPSOMATIC}/savedmodels/deepsomatic.ont.savedmodel/fingerprint.pb .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepSomatic/${VERSION_DEEPSOMATIC}/savedmodels/deepsomatic.ont.savedmodel/saved_model.pb .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepSomatic/${VERSION_DEEPSOMATIC}/savedmodels/deepsomatic.ont.savedmodel/example_info.json .





  
  

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WORKDIR /opt/models/deepsomatic/ont/variables





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepSomatic/${VERSION_DEEPSOMATIC}/savedmodels/deepsomatic.ont.savedmodel/variables/variables.data-00000-of-00001 .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepSomatic/${VERSION_DEEPSOMATIC}/savedmodels/deepsomatic.ont.savedmodel/variables/variables.index .





  
  

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RUN chmod -R +r /opt/models/deepsomatic/ont/*





  
  

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WORKDIR /opt/models/deepsomatic/ffpe_wgs





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepSomatic/${VERSION_DEEPSOMATIC}/savedmodels/deepsomatic.ffpe_wgs.savedmodel/fingerprint.pb .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepSomatic/${VERSION_DEEPSOMATIC}/savedmodels/deepsomatic.ffpe_wgs.savedmodel/saved_model.pb .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepSomatic/${VERSION_DEEPSOMATIC}/savedmodels/deepsomatic.ffpe_wgs.savedmodel/example_info.json .





  
  

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WORKDIR /opt/models/deepsomatic/ffpe_wgs/variables





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepSomatic/${VERSION_DEEPSOMATIC}/savedmodels/deepsomatic.ffpe_wgs.savedmodel/variables/variables.data-00000-of-00001 .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepSomatic/${VERSION_DEEPSOMATIC}/savedmodels/deepsomatic.ffpe_wgs.savedmodel/variables/variables.index .





  
  

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RUN chmod -R +r /opt/models/deepsomatic/ffpe_wgs/*





  
  

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WORKDIR /opt/models/deepsomatic/ffpe_wes





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepSomatic/${VERSION_DEEPSOMATIC}/savedmodels/deepsomatic.ffpe_wes.savedmodel/fingerprint.pb .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepSomatic/${VERSION_DEEPSOMATIC}/savedmodels/deepsomatic.ffpe_wes.savedmodel/saved_model.pb .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepSomatic/${VERSION_DEEPSOMATIC}/savedmodels/deepsomatic.ffpe_wes.savedmodel/example_info.json .





  
  

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WORKDIR /opt/models/deepsomatic/ffpe_wes/variables





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepSomatic/${VERSION_DEEPSOMATIC}/savedmodels/deepsomatic.ffpe_wes.savedmodel/variables/variables.data-00000-of-00001 .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepSomatic/${VERSION_DEEPSOMATIC}/savedmodels/deepsomatic.ffpe_wes.savedmodel/variables/variables.index .





  
  

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RUN chmod -R +r /opt/models/deepsomatic/ffpe_wes/*





  
  

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# Tumor-only models





  
  

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WORKDIR /opt/models/deepsomatic/wgs_tumor_only





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepSomatic/${VERSION_DEEPSOMATIC}/savedmodels/deepsomatic.wgs_tumor_only.savedmodel/fingerprint.pb .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepSomatic/${VERSION_DEEPSOMATIC}/savedmodels/deepsomatic.wgs_tumor_only.savedmodel/saved_model.pb .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepSomatic/${VERSION_DEEPSOMATIC}/savedmodels/deepsomatic.wgs_tumor_only.savedmodel/example_info.json .





  
  

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WORKDIR /opt/models/deepsomatic/wgs_tumor_only/variables





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepSomatic/${VERSION_DEEPSOMATIC}/savedmodels/deepsomatic.wgs_tumor_only.savedmodel/variables/variables.data-00000-of-00001 .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepSomatic/${VERSION_DEEPSOMATIC}/savedmodels/deepsomatic.wgs_tumor_only.savedmodel/variables/variables.index .





  
  

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RUN chmod -R +r /opt/models/deepsomatic/wgs_tumor_only/*





  
  

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WORKDIR /opt/models/deepsomatic/pacbio_tumor_only





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepSomatic/${VERSION_DEEPSOMATIC}/savedmodels/deepsomatic.pacbio_tumor_only.savedmodel/fingerprint.pb .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepSomatic/${VERSION_DEEPSOMATIC}/savedmodels/deepsomatic.pacbio_tumor_only.savedmodel/saved_model.pb .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepSomatic/${VERSION_DEEPSOMATIC}/savedmodels/deepsomatic.pacbio_tumor_only.savedmodel/example_info.json .





  
  

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WORKDIR /opt/models/deepsomatic/pacbio_tumor_only/variables





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepSomatic/${VERSION_DEEPSOMATIC}/savedmodels/deepsomatic.pacbio_tumor_only.savedmodel/variables/variables.data-00000-of-00001 .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepSomatic/${VERSION_DEEPSOMATIC}/savedmodels/deepsomatic.pacbio_tumor_only.savedmodel/variables/variables.index .





  
  

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RUN chmod -R +r /opt/models/deepsomatic/pacbio_tumor_only/*





  
  

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WORKDIR /opt/models/deepsomatic/ont_tumor_only





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepSomatic/${VERSION_DEEPSOMATIC}/savedmodels/deepsomatic.ont_tumor_only.savedmodel/fingerprint.pb .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepSomatic/${VERSION_DEEPSOMATIC}/savedmodels/deepsomatic.ont_tumor_only.savedmodel/saved_model.pb .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepSomatic/${VERSION_DEEPSOMATIC}/savedmodels/deepsomatic.ont_tumor_only.savedmodel/example_info.json .





  
  

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WORKDIR /opt/models/deepsomatic/ont_tumor_only/variables





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepSomatic/${VERSION_DEEPSOMATIC}/savedmodels/deepsomatic.ont_tumor_only.savedmodel/variables/variables.data-00000-of-00001 .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepSomatic/${VERSION_DEEPSOMATIC}/savedmodels/deepsomatic.ont_tumor_only.savedmodel/variables/variables.index .





  
  

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RUN chmod -R +r /opt/models/deepsomatic/ont_tumor_only/*





  
  

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# PONs and AF VCF files





  
  

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WORKDIR /opt/models/deepsomatic/pons





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepSomatic/${VERSION_DEEPSOMATIC}/pons/AF_ilmn_PON_DeepVariant.GRCh38.AF0.05.vcf.gz .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepSomatic/${VERSION_DEEPSOMATIC}/pons/AF_ilmn_PON_DeepVariant.GRCh38.AF0.05.vcf.gz.tbi .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepSomatic/${VERSION_DEEPSOMATIC}/pons/AF_pacbio_PON_CoLoRSdb.GRCh38.AF0.05.vcf.gz .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepSomatic/${VERSION_DEEPSOMATIC}/pons/AF_pacbio_PON_CoLoRSdb.GRCh38.AF0.05.vcf.gz.tbi .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepSomatic/${VERSION_DEEPSOMATIC}/pons/PON_dbsnp138_gnomad_ILMN1000g_pon.vcf.gz .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepSomatic/${VERSION_DEEPSOMATIC}/pons/PON_dbsnp138_gnomad_ILMN1000g_pon.vcf.gz.tbi .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepSomatic/${VERSION_DEEPSOMATIC}/pons/PON_dbsnp138_gnomad_PB1000g_pon.vcf.gz .





  
  

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ADD https://storage.googleapis.com/deepvariant/models/DeepSomatic/${VERSION_DEEPSOMATIC}/pons/PON_dbsnp138_gnomad_PB1000g_pon.vcf.gz.tbi .





  
  

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RUN chmod -R +r /opt/models/deepsomatic/pons/*





  
  

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ENV PATH="${PATH}":/opt/conda/bin:/opt/conda/envs/bio/bin:/opt/deepvariant/bin/deepsomatic:/opt/deepvariant/bin





  
  

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RUN apt-get -y update && \





  
  

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  apt-get install -y parallel python3-pip && \





  
  

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  PATH="${HOME}/.local/bin:$PATH" python3 -m pip install absl-py==0.13.0 && \





  
  

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  apt-get clean autoclean && \





  
  

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  apt-get autoremove -y --purge && \





  
  

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  rm -rf /var/lib/apt/lists/*





  
  

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WORKDIR /opt/deepvariant





  
  

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CMD ["/opt/deepvariant/bin/deepsomatic/run_deepsomatic", "--help"]