forked from google/deepvariant
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathDockerfile.deeptrio
147 lines (123 loc) · 7.66 KB
/
Dockerfile.deeptrio
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
# 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:11.3.0-cudnn8-devel-ubuntu20.04 --build-arg=DV_GPU_BUILD=1 -t deeptrio_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_DEEPTRIO=1.2.0
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
WORKDIR /opt/deepvariant
RUN ./build-prereq.sh \
&& PATH="${HOME}/bin:${PATH}" ./build_release_binaries.sh # PATH for bazel
FROM ${FROM_IMAGE}
ARG DV_GPU_BUILD
ARG VERSION_DEEPTRIO
ARG PYTHON_VERSION
ENV DV_GPU_BUILD=${DV_GPU_BUILD}
ENV VERSION_DEEPTRIO ${VERSION_DEEPTRIO}
ENV PYTHON_VERSION ${PYTHON_VERSION}
WORKDIR /opt/
COPY --from=builder /opt/deepvariant/bazel-bin/licenses.zip .
WORKDIR /opt/deepvariant/bin/
COPY --from=builder /opt/conda /opt/conda
COPY --from=builder /opt/deepvariant/run-prereq.sh .
COPY --from=builder /opt/deepvariant/settings.sh .
COPY --from=builder /opt/deepvariant/bazel-out/k8-opt/bin/deepvariant/call_variants.zip .
COPY --from=builder /opt/deepvariant/bazel-out/k8-opt/bin/deepvariant/postprocess_variants.zip .
COPY --from=builder /opt/deepvariant/bazel-out/k8-opt/bin/deepvariant/runtime_by_region_vis.zip .
COPY --from=builder /opt/deepvariant/scripts/run_deeptrio.py ./deeptrio/
COPY --from=builder /opt/deepvariant/bazel-out/k8-opt/bin/deeptrio/make_examples.zip ./deeptrio/
RUN ./run-prereq.sh
RUN update-alternatives --install /usr/bin/python3 python3 /usr/bin/python${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/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 /opt/deepvariant/bin/runtime_by_region_vis.zip "$@"' > \
/opt/deepvariant/bin/runtime_by_region_vis && \
printf "%s\n%s\n" \
"${BASH_HEADER}" \
'python3 -u /opt/deepvariant/bin/deeptrio/run_deeptrio.py "$@"' > \
/opt/deepvariant/bin/deeptrio/run_deeptrio && \
chmod +x /opt/deepvariant/bin/deeptrio/make_examples \
/opt/deepvariant/bin/call_variants \
/opt/deepvariant/bin/postprocess_variants \
/opt/deepvariant/bin/runtime_by_region_vis \
/opt/deepvariant/bin/deeptrio/run_deeptrio
# Copy models
WORKDIR /opt/models/deeptrio/wgs/child
ADD https://storage.googleapis.com/deepvariant/models/DeepTrio/${VERSION_DEEPTRIO}/DeepTrio-inception_v3-${VERSION_DEEPTRIO}+data-wgs_child_standard/model.ckpt.data-00000-of-00001 .
ADD https://storage.googleapis.com/deepvariant/models/DeepTrio/${VERSION_DEEPTRIO}/DeepTrio-inception_v3-${VERSION_DEEPTRIO}+data-wgs_child_standard/model.ckpt.index .
ADD https://storage.googleapis.com/deepvariant/models/DeepTrio/${VERSION_DEEPTRIO}/DeepTrio-inception_v3-${VERSION_DEEPTRIO}+data-wgs_child_standard/model.ckpt.meta .
RUN chmod +r /opt/models/deeptrio/wgs/child/model.ckpt*
WORKDIR /opt/models/deeptrio/wgs/parent
ADD https://storage.googleapis.com/deepvariant/models/DeepTrio/${VERSION_DEEPTRIO}/DeepTrio-inception_v3-${VERSION_DEEPTRIO}+data-wgs_parent_standard/model.ckpt.data-00000-of-00001 .
ADD https://storage.googleapis.com/deepvariant/models/DeepTrio/${VERSION_DEEPTRIO}/DeepTrio-inception_v3-${VERSION_DEEPTRIO}+data-wgs_parent_standard/model.ckpt.index .
ADD https://storage.googleapis.com/deepvariant/models/DeepTrio/${VERSION_DEEPTRIO}/DeepTrio-inception_v3-${VERSION_DEEPTRIO}+data-wgs_parent_standard/model.ckpt.meta .
RUN chmod +r /opt/models/deeptrio/wgs/parent/model.ckpt*
WORKDIR /opt/models/deeptrio/pacbio/child
ADD https://storage.googleapis.com/deepvariant/models/DeepTrio/${VERSION_DEEPTRIO}/DeepTrio-inception_v3-${VERSION_DEEPTRIO}+data-pacbio_child_standard/model.ckpt.data-00000-of-00001 .
ADD https://storage.googleapis.com/deepvariant/models/DeepTrio/${VERSION_DEEPTRIO}/DeepTrio-inception_v3-${VERSION_DEEPTRIO}+data-pacbio_child_standard/model.ckpt.index .
ADD https://storage.googleapis.com/deepvariant/models/DeepTrio/${VERSION_DEEPTRIO}/DeepTrio-inception_v3-${VERSION_DEEPTRIO}+data-pacbio_child_standard/model.ckpt.meta .
RUN chmod +r /opt/models/deeptrio/pacbio/child/model.ckpt*
WORKDIR /opt/models/deeptrio/pacbio/parent
ADD https://storage.googleapis.com/deepvariant/models/DeepTrio/${VERSION_DEEPTRIO}/DeepTrio-inception_v3-${VERSION_DEEPTRIO}+data-pacbio_parent_standard/model.ckpt.data-00000-of-00001 .
ADD https://storage.googleapis.com/deepvariant/models/DeepTrio/${VERSION_DEEPTRIO}/DeepTrio-inception_v3-${VERSION_DEEPTRIO}+data-pacbio_parent_standard/model.ckpt.index .
ADD https://storage.googleapis.com/deepvariant/models/DeepTrio/${VERSION_DEEPTRIO}/DeepTrio-inception_v3-${VERSION_DEEPTRIO}+data-pacbio_parent_standard/model.ckpt.meta .
RUN chmod +r /opt/models/deeptrio/pacbio/parent/model.ckpt*
WORKDIR /opt/models/deeptrio/wes/child
ADD https://storage.googleapis.com/deepvariant/models/DeepTrio/${VERSION_DEEPTRIO}/DeepTrio-inception_v3-${VERSION_DEEPTRIO}+data-wes_child_standard/model.ckpt.data-00000-of-00001 .
ADD https://storage.googleapis.com/deepvariant/models/DeepTrio/${VERSION_DEEPTRIO}/DeepTrio-inception_v3-${VERSION_DEEPTRIO}+data-wes_child_standard/model.ckpt.index .
ADD https://storage.googleapis.com/deepvariant/models/DeepTrio/${VERSION_DEEPTRIO}/DeepTrio-inception_v3-${VERSION_DEEPTRIO}+data-wes_child_standard/model.ckpt.meta .
RUN chmod +r /opt/models/deeptrio/wes/child/model.ckpt*
WORKDIR /opt/models/deeptrio/wes/parent
ADD https://storage.googleapis.com/deepvariant/models/DeepTrio/${VERSION_DEEPTRIO}/DeepTrio-inception_v3-${VERSION_DEEPTRIO}+data-wes_parent_standard/model.ckpt.data-00000-of-00001 .
ADD https://storage.googleapis.com/deepvariant/models/DeepTrio/${VERSION_DEEPTRIO}/DeepTrio-inception_v3-${VERSION_DEEPTRIO}+data-wes_parent_standard/model.ckpt.index .
ADD https://storage.googleapis.com/deepvariant/models/DeepTrio/${VERSION_DEEPTRIO}/DeepTrio-inception_v3-${VERSION_DEEPTRIO}+data-wes_parent_standard/model.ckpt.meta .
RUN chmod +r /opt/models/deeptrio/wes/parent/model.ckpt*
ENV PATH="${PATH}":/opt/conda/bin:/opt/conda/envs/bio/bin:/opt/deepvariant/bin/deeptrio:/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/deeptrio/run_deeptrio", "--help"]