-
Notifications
You must be signed in to change notification settings - Fork 728
/
Dockerfile
213 lines (187 loc) · 10.5 KB
/
Dockerfile
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
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
# 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"]