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Catherine Stones
cathy-stones/
deepvariant-r1.6.1
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# Copyright 2019 Google LLC.

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

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

# to the code.

# Example command:

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

# $ cd deepvariant

# $ sudo docker build -t deepvariant .

#

# To build for GPU, use a command like:

# $ sudo docker build --build-arg=FROM_IMAGE=nvidia/cuda:11.3.1-cudnn8-devel-ubuntu20.04 --build-arg=DV_GPU_BUILD=1 -t deepvariant_gpu .





ARG FROM_IMAGE=ubuntu:20.04

# PYTHON_VERSION is also set in settings.sh.

ARG PYTHON_VERSION=3.8

ARG DV_GPU_BUILD=0

ARG VERSION=1.6.0



FROM continuumio/miniconda3 as conda_setup

RUN conda config --add channels defaults && \

    conda config --add channels bioconda && \

    conda config --add channels conda-forge

RUN conda create -n bio \

                    bioconda::bcftools=1.10 \

                    bioconda::samtools=1.10 \

    && conda clean -a



FROM ${FROM_IMAGE} as builder

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

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



ARG DV_GPU_BUILD

ENV DV_GPU_BUILD=${DV_GPU_BUILD}



# Copying DeepVariant source code

COPY . /opt/deepvariant



ARG VERSION

ENV VERSION=${VERSION}



WORKDIR /opt/deepvariant



RUN echo "Acquire::http::proxy \"$http_proxy\";\n" \

         "Acquire::https::proxy \"$https_proxy\";" > "/etc/apt/apt.conf"



RUN ./build-prereq.sh \

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



FROM ${FROM_IMAGE}

ARG DV_GPU_BUILD

ARG VERSION

ARG PYTHON_VERSION

ENV DV_GPU_BUILD=${DV_GPU_BUILD}

ENV VERSION ${VERSION}

ENV PYTHON_VERSION ${PYTHON_VERSION}



RUN echo "Acquire::http::proxy \"$http_proxy\";\n" \

         "Acquire::https::proxy \"$https_proxy\";" > "/etc/apt/apt.conf"



WORKDIR /opt/

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



WORKDIR /opt/deepvariant/bin/

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

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

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

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

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

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

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

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

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

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

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

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

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

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

COPY --from=builder /opt/deepvariant/scripts/run_deepvariant.py .

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



RUN ./run-prereq.sh



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

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



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

RUN \

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

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

    "${BASH_HEADER}" \

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

    /opt/deepvariant/bin/make_examples && \

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

    "${BASH_HEADER}" \

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

    /opt/deepvariant/bin/call_variants && \

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

    "${BASH_HEADER}" \

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

    /opt/deepvariant/bin/call_variants_slim && \

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

    "${BASH_HEADER}" \

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

    /opt/deepvariant/bin/postprocess_variants && \

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

    "${BASH_HEADER}" \

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

    /opt/deepvariant/bin/vcf_stats_report && \

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

    "${BASH_HEADER}" \

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

    /opt/deepvariant/bin/show_examples && \

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

    "${BASH_HEADER}" \

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

    /opt/deepvariant/bin/runtime_by_region_vis && \

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

    "${BASH_HEADER}" \

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

    /opt/deepvariant/bin/multisample_make_examples && \

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

    "${BASH_HEADER}" \

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

    /opt/deepvariant/bin/labeled_examples_to_vcf && \

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

    "${BASH_HEADER}" \

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

    /opt/deepvariant/bin/make_examples_somatic && \

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

    "${BASH_HEADER}" \

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

    /opt/deepvariant/bin/run_deepvariant && \

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

    "${BASH_HEADER}" \

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

    /opt/deepvariant/bin/run_deepsomatic && \

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

    "${BASH_HEADER}" \

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

    /opt/deepvariant/bin/train && \

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

    /opt/deepvariant/bin/call_variants \

    /opt/deepvariant/bin/call_variants_slim \

    /opt/deepvariant/bin/postprocess_variants \

    /opt/deepvariant/bin/vcf_stats_report \

    /opt/deepvariant/bin/show_examples \

    /opt/deepvariant/bin/runtime_by_region_vis \

    /opt/deepvariant/bin/multisample_make_examples \

    /opt/deepvariant/bin/run_deepvariant \

    /opt/deepvariant/bin/run_deepsomatic \

    /opt/deepvariant/bin/labeled_examples_to_vcf \

    /opt/deepvariant/bin/make_examples_somatic \

    /opt/deepvariant/bin/train



# Copy models

WORKDIR /opt/models/wgs

ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/savedmodels/deepvariant.wgs.savedmodel/fingerprint.pb .

ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/savedmodels/deepvariant.wgs.savedmodel/saved_model.pb .

ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/savedmodels/deepvariant.wgs.savedmodel/example_info.json .

WORKDIR /opt/models/wgs/variables

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

ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/savedmodels/deepvariant.wgs.savedmodel/variables/variables.index .

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



WORKDIR /opt/models/wes

ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/savedmodels/deepvariant.wes.savedmodel/fingerprint.pb .

ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/savedmodels/deepvariant.wes.savedmodel/saved_model.pb .

ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/savedmodels/deepvariant.wes.savedmodel/example_info.json .

WORKDIR /opt/models/wes/variables

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

ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/savedmodels/deepvariant.wes.savedmodel/variables/variables.index .

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



WORKDIR /opt/models/pacbio

ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/savedmodels/deepvariant.pacbio.savedmodel/fingerprint.pb .

ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/savedmodels/deepvariant.pacbio.savedmodel/saved_model.pb .

ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/savedmodels/deepvariant.pacbio.savedmodel/example_info.json .

WORKDIR /opt/models/pacbio/variables

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

ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/savedmodels/deepvariant.pacbio.savedmodel/variables/variables.index .

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



WORKDIR /opt/models/hybrid_pacbio_illumina

ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/savedmodels/deepvariant.hybrid.savedmodel/fingerprint.pb .

ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/savedmodels/deepvariant.hybrid.savedmodel/saved_model.pb .

ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/savedmodels/deepvariant.hybrid.savedmodel/example_info.json .

WORKDIR /opt/models/hybrid_pacbio_illumina/variables

ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/savedmodels/deepvariant.hybrid.savedmodel/variables/variables.data-00000-of-00001 .

ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/savedmodels/deepvariant.hybrid.savedmodel/variables/variables.index .

RUN chmod -R +r /opt/models/hybrid_pacbio_illumina/*



WORKDIR /opt/models/ont_r104

ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/savedmodels/deepvariant.ont.savedmodel/fingerprint.pb .

ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/savedmodels/deepvariant.ont.savedmodel/saved_model.pb .

ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/savedmodels/deepvariant.ont.savedmodel/example_info.json .

WORKDIR /opt/models/ont_r104/variables

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

ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/savedmodels/deepvariant.ont.savedmodel/variables/variables.index .

RUN chmod -R +r /opt/models/ont_r104/*



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



RUN apt-get -y update && \

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

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

  apt-get clean autoclean && \

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

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



WORKDIR /opt/deepvariant



CMD ["/opt/deepvariant/bin/run_deepvariant", "--help"]