# Copyright 2019 Google LLC.

# This is used to build the pangenome-aware 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 -f Dockerfile.pangenome_aware_deepvariant -t pangenome_aware_deepvariant .

#

# To build for GPU, use a command like:

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

ARG FROM_IMAGE=ubuntu:22.04

# PYTHON_VERSION is also set in settings.sh.

ARG PYTHON_VERSION=3.10

ARG DV_GPU_BUILD=0

ARG VERSION_DEEPVARIANT=1.8.0

ARG TF_ENABLE_ONEDNN_OPTS=1

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=1.15 \

                    bioconda::samtools=1.15 \

    && 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

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_DEEPVARIANT

ARG PYTHON_VERSION

ARG TF_ENABLE_ONEDNN_OPTS

ENV DV_GPU_BUILD=${DV_GPU_BUILD}

ENV VERSION_DEEPVARIANT=${VERSION_DEEPVARIANT}

ENV PYTHON_VERSION=${PYTHON_VERSION}

ENV TF_ENABLE_ONEDNN_OPTS=${TF_ENABLE_ONEDNN_OPTS}

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_pangenome_aware_dv.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/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/load_gbz_into_shared_memory.zip  .

COPY --from=builder /opt/deepvariant/scripts/run_pangenome_aware_deepvariant.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 -u /opt/deepvariant/bin/make_examples_pangenome_aware_dv.zip "$@"' > \

    /opt/deepvariant/bin/make_examples_pangenome_aware_dv && \

  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 /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/load_gbz_into_shared_memory.zip "$@"' > \

    /opt/deepvariant/bin/load_gbz_into_shared_memory && \

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

    "${BASH_HEADER}" \

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

    /opt/deepvariant/bin/run_pangenome_aware_deepvariant && \

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

    /opt/deepvariant/bin/call_variants \

    /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/load_gbz_into_shared_memory \

    /opt/deepvariant/bin/run_pangenome_aware_deepvariant

# Copy models

WORKDIR /opt/models/pangenome_aware_deepvariant/wgs

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

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

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

WORKDIR /opt/models/pangenome_aware_deepvariant/wgs/variables

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

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

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

WORKDIR /opt/models/pangenome_aware_deepvariant/wes

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

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

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

WORKDIR /opt/models/pangenome_aware_deepvariant/wes/variables

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

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

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

ENV PATH="${PATH}":/opt/conda/bin:/opt/conda/envs/bio/bin:/opt/deepvariant/bin/pangenome_aware_deepvariant:/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_pangenome_aware_deepvariant", "--help"]