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Dockerfile.deeptrio
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# Copyright 2019 Google LLC.
# This is used to build the DeepTrio 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 -f Dockerfile.deeptrio -t deeptrio .
#
# To build for GPU, use a command like:
# $ sudo docker build -f Dockerfile.deeptrio --build-arg=FROM_IMAGE=nvidia/cuda:10.1-cudnn7-devel-ubuntu18.04 --build-arg=DV_GPU_BUILD=1 -t deeptrio_gpu .
ARG FROM_IMAGE=ubuntu:18.04
ARG DV_GPU_BUILD=0
ARG VERSION_DEEPTRIO=1.1.0
ARG FULL_VERSION_DEEPTRIO=1.1.0
FROM ${FROM_IMAGE} as builder
LABEL maintainer="https://github.com/google/deepvariant/issues"
ARG DV_GPU_BUILD
ENV DV_GPU_BUILD=${DV_GPU_BUILD}
# Copying DeepVariant source code
COPY . /opt/deepvariant
WORKDIR /opt/deepvariant
RUN ./build-prereq.sh \
&& PATH="${HOME}/bin:${PATH}" ./build_release_binaries.sh # PATH for bazel
FROM ${FROM_IMAGE}
ARG DV_GPU_BUILD
ARG VERSION_DEEPTRIO
ARG FULL_VERSION_DEEPTRIO
ENV DV_GPU_BUILD=${DV_GPU_BUILD}
ENV VERSION_DEEPTRIO ${VERSION_DEEPTRIO}
ENV FULL_VERSION_DEEPTRIO ${FULL_VERSION_DEEPTRIO}
WORKDIR /opt/
COPY --from=builder /opt/deepvariant/bazel-bin/licenses.zip .
WORKDIR /opt/deepvariant/bin/
COPY --from=builder /opt/deepvariant/run-prereq.sh .
COPY --from=builder /opt/deepvariant/settings.sh .
COPY --from=builder /opt/deepvariant/bazel-out/k8-opt/bin/deepvariant/call_variants.zip .
COPY --from=builder /opt/deepvariant/bazel-out/k8-opt/bin/deepvariant/postprocess_variants.zip .
COPY --from=builder /opt/deepvariant/scripts/run_deeptrio.py ./deeptrio/
COPY --from=builder /opt/deepvariant/bazel-out/k8-opt/bin/deeptrio/make_examples.zip ./deeptrio/
RUN ./run-prereq.sh
# Make python3.6 default.
RUN update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.6 0 && \
update-alternatives --install /usr/bin/python python /usr/bin/python3.6 0
# Create shell wrappers for python zip files for easier use.
RUN \
BASH_HEADER='#!/bin/bash' && \
printf "%s\n%s\n" \
"${BASH_HEADER}" \
'python3 /opt/deepvariant/bin/deeptrio/make_examples.zip "$@"' > \
/opt/deepvariant/bin/deeptrio/make_examples && \
printf "%s\n%s\n" \
"${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/postprocess_variants.zip "$@"' > \
/opt/deepvariant/bin/postprocess_variants && \
printf "%s\n%s\n" \
"${BASH_HEADER}" \
'python3 -u /opt/deepvariant/bin/deeptrio/run_deeptrio.py "$@"' > \
/opt/deepvariant/bin/deeptrio/run_deeptrio && \
chmod +x /opt/deepvariant/bin/deeptrio/make_examples \
/opt/deepvariant/bin/call_variants \
/opt/deepvariant/bin/postprocess_variants \
/opt/deepvariant/bin/deeptrio/run_deeptrio
# Copy models
WORKDIR /opt/models/deeptrio/wgs/child
ADD https://storage.googleapis.com/deepvariant/models/DeepTrio/${VERSION_DEEPTRIO}/DeepTrio-inception_v3-${FULL_VERSION_DEEPTRIO}+data-wgs_child_standard/model.ckpt.data-00000-of-00001 .
ADD https://storage.googleapis.com/deepvariant/models/DeepTrio/${VERSION_DEEPTRIO}/DeepTrio-inception_v3-${FULL_VERSION_DEEPTRIO}+data-wgs_child_standard/model.ckpt.index .
ADD https://storage.googleapis.com/deepvariant/models/DeepTrio/${VERSION_DEEPTRIO}/DeepTrio-inception_v3-${FULL_VERSION_DEEPTRIO}+data-wgs_child_standard/model.ckpt.meta .
RUN chmod +r /opt/models/deeptrio/wgs/child/model.ckpt*
WORKDIR /opt/models/deeptrio/wgs/parent
ADD https://storage.googleapis.com/deepvariant/models/DeepTrio/${VERSION_DEEPTRIO}/DeepTrio-inception_v3-${FULL_VERSION_DEEPTRIO}+data-wgs_parent_standard/model.ckpt.data-00000-of-00001 .
ADD https://storage.googleapis.com/deepvariant/models/DeepTrio/${VERSION_DEEPTRIO}/DeepTrio-inception_v3-${FULL_VERSION_DEEPTRIO}+data-wgs_parent_standard/model.ckpt.index .
ADD https://storage.googleapis.com/deepvariant/models/DeepTrio/${VERSION_DEEPTRIO}/DeepTrio-inception_v3-${FULL_VERSION_DEEPTRIO}+data-wgs_parent_standard/model.ckpt.meta .
RUN chmod +r /opt/models/deeptrio/wgs/parent/model.ckpt*
WORKDIR /opt/models/deeptrio/pacbio/child
ADD https://storage.googleapis.com/deepvariant/models/DeepTrio/${VERSION_DEEPTRIO}/DeepTrio-inception_v3-${FULL_VERSION_DEEPTRIO}+data-pacbio_child_standard/model.ckpt.data-00000-of-00001 .
ADD https://storage.googleapis.com/deepvariant/models/DeepTrio/${VERSION_DEEPTRIO}/DeepTrio-inception_v3-${FULL_VERSION_DEEPTRIO}+data-pacbio_child_standard/model.ckpt.index .
ADD https://storage.googleapis.com/deepvariant/models/DeepTrio/${VERSION_DEEPTRIO}/DeepTrio-inception_v3-${FULL_VERSION_DEEPTRIO}+data-pacbio_child_standard/model.ckpt.meta .
RUN chmod +r /opt/models/deeptrio/pacbio/child/model.ckpt*
WORKDIR /opt/models/deeptrio/pacbio/parent
ADD https://storage.googleapis.com/deepvariant/models/DeepTrio/${VERSION_DEEPTRIO}/DeepTrio-inception_v3-${FULL_VERSION_DEEPTRIO}+data-pacbio_parent_standard/model.ckpt.data-00000-of-00001 .
ADD https://storage.googleapis.com/deepvariant/models/DeepTrio/${VERSION_DEEPTRIO}/DeepTrio-inception_v3-${FULL_VERSION_DEEPTRIO}+data-pacbio_parent_standard/model.ckpt.index .
ADD https://storage.googleapis.com/deepvariant/models/DeepTrio/${VERSION_DEEPTRIO}/DeepTrio-inception_v3-${FULL_VERSION_DEEPTRIO}+data-pacbio_parent_standard/model.ckpt.meta .
RUN chmod +r /opt/models/deeptrio/pacbio/parent/model.ckpt*
WORKDIR /opt/models/deeptrio/wes/child
ADD https://storage.googleapis.com/deepvariant/models/DeepTrio/${VERSION_DEEPTRIO}/DeepTrio-inception_v3-${FULL_VERSION_DEEPTRIO}+data-wes_child_standard/model.ckpt.data-00000-of-00001 .
ADD https://storage.googleapis.com/deepvariant/models/DeepTrio/${VERSION_DEEPTRIO}/DeepTrio-inception_v3-${FULL_VERSION_DEEPTRIO}+data-wes_child_standard/model.ckpt.index .
ADD https://storage.googleapis.com/deepvariant/models/DeepTrio/${VERSION_DEEPTRIO}/DeepTrio-inception_v3-${FULL_VERSION_DEEPTRIO}+data-wes_child_standard/model.ckpt.meta .
RUN chmod +r /opt/models/deeptrio/wes/child/model.ckpt*
WORKDIR /opt/models/deeptrio/wes/parent
ADD https://storage.googleapis.com/deepvariant/models/DeepTrio/${VERSION_DEEPTRIO}/DeepTrio-inception_v3-${FULL_VERSION_DEEPTRIO}+data-wes_parent_standard/model.ckpt.data-00000-of-00001 .
ADD https://storage.googleapis.com/deepvariant/models/DeepTrio/${VERSION_DEEPTRIO}/DeepTrio-inception_v3-${FULL_VERSION_DEEPTRIO}+data-wes_parent_standard/model.ckpt.index .
ADD https://storage.googleapis.com/deepvariant/models/DeepTrio/${VERSION_DEEPTRIO}/DeepTrio-inception_v3-${FULL_VERSION_DEEPTRIO}+data-wes_parent_standard/model.ckpt.meta .
RUN chmod +r /opt/models/deeptrio/wes/parent/model.ckpt*
RUN apt-get -y update && \
apt-get install -y parallel python3-pip samtools && \
PATH="${HOME}/.local/bin:$PATH" python3 -m pip install absl-py==0.8.1 && \
apt-get clean autoclean && \
apt-get autoremove -y --purge && \
rm -rf /var/lib/apt/lists/*
ENV PATH="/opt/deepvariant/bin/deeptrio:/opt/deepvariant/bin:${PATH}"
WORKDIR /opt/deepvariant
CMD ["/opt/deepvariant/bin/deeptrio/run_deeptrio", "--help"]