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Dockerfile
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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"]