-
Notifications
You must be signed in to change notification settings - Fork 10
/
Dockerfile
289 lines (259 loc) · 11.2 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
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
# NiBabies Docker Container Image distribution
#
# MIT License
#
# Copyright (c) 2023 The NiPreps Developers
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in all
# copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
# Ubuntu 22.04 LTS - Jammy
ARG BASE_IMAGE=ubuntu:jammy-20240405
# NiBabies wheel
FROM python:slim AS src
RUN pip install build
RUN apt-get update && \
apt-get install -y --no-install-recommends git
COPY . /src
RUN python -m build /src
# Older Python to support legacy MCRIBS
FROM python:3.6.15-slim as pyenv
RUN pip install --no-cache-dir numpy nibabel scipy pandas numexpr contextlib2 \
&& cp /usr/lib/x86_64-linux-gnu/libffi.so.7* /usr/local/lib
# Intermediate step with utilities for downloading packages
FROM ${BASE_IMAGE} as downloader
RUN apt-get update && \
apt-get install -y --no-install-recommends \
binutils \
bzip2 \
ca-certificates \
curl \
unzip && \
apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
# AFNI
FROM downloader as afni
# The download link can point to newer releases
# As a safeguard, take advantage of Docker caching, and
# Bump the date to current to update AFNI
RUN echo "2023.06.09"
RUN mkdir -p /opt/afni-latest \
&& curl -fsSL --retry 5 https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz \
| tar -xz -C /opt/afni-latest --strip-components 1 \
--exclude "linux_openmp_64/*.gz" \
--exclude "linux_openmp_64/funstuff" \
--exclude "linux_openmp_64/shiny" \
--exclude "linux_openmp_64/afnipy" \
--exclude "linux_openmp_64/lib/RetroTS" \
--exclude "linux_openmp_64/lib_RetroTS" \
--exclude "linux_openmp_64/meica.libs" \
# Keep only what we use
&& find /opt/afni-latest -type f -not \( \
-name "3dTshift" -or \
-name "3dUnifize" -or \
-name "3dAutomask" -or \
-name "3dvolreg" \) -delete
# ANTs 2.4.4
FROM downloader as ants
RUN mkdir -p /opt && \
curl -sSLO "https://github.com/ANTsX/ANTs/releases/download/v2.4.4/ants-2.4.4-ubuntu-22.04-X64-gcc.zip" && \
unzip ants-2.4.4-ubuntu-22.04-X64-gcc.zip -d /opt && \
rm ants-2.4.4-ubuntu-22.04-X64-gcc.zip
# Connectome Workbench 1.5.0
FROM downloader as workbench
RUN mkdir /opt/workbench && \
curl -sSLO https://www.humanconnectome.org/storage/app/media/workbench/workbench-linux64-v1.5.0.zip && \
unzip workbench-linux64-v1.5.0.zip -d /opt && \
rm workbench-linux64-v1.5.0.zip && \
rm -rf /opt/workbench/libs_linux64_software_opengl /opt/workbench/plugins_linux64 && \
strip --remove-section=.note.ABI-tag /opt/workbench/libs_linux64/libQt5Core.so.5
# Micromamba
FROM downloader as micromamba
# Install a C compiler to build extensions when needed.
# traits<6.4 wheels are not available for Python 3.11+, but build easily.
RUN apt-get update && \
apt-get install -y --no-install-recommends build-essential && \
apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
WORKDIR /
# Bump the date to current to force update micromamba
RUN echo "2024.04.25" && curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj bin/micromamba
ENV MAMBA_ROOT_PREFIX="/opt/conda"
COPY env.yml /tmp/env.yml
COPY requirements.txt /tmp/requirements.txt
WORKDIR /tmp
RUN micromamba create -y -f /tmp/env.yml && \
micromamba clean -y -a
ENV PATH="/opt/conda/envs/nibabies/bin:$PATH"
RUN npm install -g svgo@^3.2.0 [email protected] && \
rm -r ~/.npm
# Main container
FROM ${BASE_IMAGE} as nibabies
ENV DEBIAN_FRONTEND="noninteractive" \
LANG="en_US.UTF-8" \
LC_ALL="en_US.UTF-8"
# Prepare environment
RUN apt-get update && \
apt-get install -y --no-install-recommends \
apt-utils \
bc \
build-essential \
ca-certificates \
curl \
git \
gnupg \
libtool \
locales \
lsb-release \
netbase \
unzip \
xvfb \
# MCRIBS-required
libboost-dev \
libeigen3-dev \
libflann-dev \
libgl1-mesa-dev \
libglu1-mesa-dev \
libssl-dev \
libxt-dev \
zlib1g-dev && \
locale-gen en_US.UTF-8 && \
apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
# Configure PPAs for libpng12 and libxp6
RUN GNUPGHOME=/tmp gpg --keyserver hkps://keyserver.ubuntu.com --no-default-keyring --keyring /usr/share/keyrings/linuxuprising.gpg --recv 0xEA8CACC073C3DB2A \
&& GNUPGHOME=/tmp gpg --keyserver hkps://keyserver.ubuntu.com --no-default-keyring --keyring /usr/share/keyrings/zeehio.gpg --recv 0xA1301338A3A48C4A \
&& echo "deb [signed-by=/usr/share/keyrings/linuxuprising.gpg] https://ppa.launchpadcontent.net/linuxuprising/libpng12/ubuntu jammy main" > /etc/apt/sources.list.d/linuxuprising.list \
&& echo "deb [signed-by=/usr/share/keyrings/zeehio.gpg] https://ppa.launchpadcontent.net/zeehio/libxp/ubuntu jammy main" > /etc/apt/sources.list.d/zeehio.list
# Dependencies for AFNI; requires a discontinued multiarch-support package from bionic (18.04)
RUN apt-get update -qq \
&& apt-get install -y -q --no-install-recommends \
ed \
gsl-bin \
libglib2.0-0 \
libglu1-mesa-dev \
libglw1-mesa \
libgomp1 \
libjpeg62 \
libpng12-0 \
libxm4 \
libxp6 \
netpbm \
tcsh \
xfonts-base \
xvfb \
&& curl -sSL --retry 5 -o /tmp/multiarch.deb http://archive.ubuntu.com/ubuntu/pool/main/g/glibc/multiarch-support_2.27-3ubuntu1.5_amd64.deb \
&& dpkg -i /tmp/multiarch.deb \
&& rm /tmp/multiarch.deb \
&& apt-get install -f \
&& apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
&& gsl2_path="$(find / -name 'libgsl.so.19' || printf '')" \
&& if [ -n "$gsl2_path" ]; then \
ln -sfv "$gsl2_path" "$(dirname $gsl2_path)/libgsl.so.0"; \
fi \
&& ldconfig
COPY --from=afni /opt/afni-latest /opt/afni-latest
COPY --from=ants /opt/ants-2.4.4 /opt/ants
COPY --from=workbench /opt/workbench /opt/workbench
# AFNI config
ENV PATH="/opt/afni-latest:$PATH" \
AFNI_IMSAVE_WARNINGS="NO" \
AFNI_PLUGINPATH="/opt/afni-latest"
# ANTs config
ENV ANTSPATH="/opt/ants" \
PATH="/opt/ants/bin:$PATH" \
LD_LIBRARY_PATH="/opt/ants/lib:$LD_LIBRARY_PATH"
# Workbench config
ENV PATH="/opt/workbench/bin_linux64:$PATH" \
LD_LIBRARY_PATH="/opt/workbench/lib_linux64:$LD_LIBRARY_PATH"
# Install FreeSurfer (with Infant Module)
COPY --from=nipreps/freesurfer@sha256:3b895fc732a7080374a15c4f976510f39c0c48dc76c030ab27316febd5e419ee /opt/freesurfer /opt/freesurfer
ENV FREESURFER_HOME="/opt/freesurfer"
ENV SUBJECTS_DIR="$FREESURFER_HOME/subjects" \
FUNCTIONALS_DIR="$FREESURFER_HOME/sessions" \
MNI_DIR="$FREESURFER_HOME/mni" \
LOCAL_DIR="$FREESURFER_HOME/local" \
MINC_BIN_DIR="$FREESURFER_HOME/mni/bin" \
MINC_LIB_DIR="$FREESURFER_HOME/mni/lib" \
MNI_DATAPATH="$FREESURFER_HOME/mni/data" \
FSL_DIR=${FSLDIR} \
FREESURFER="/opt/freesurfer"
ENV PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
MNI_PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
PATH="$FREESURFER_HOME/bin:$FREESURFER_HOME/tktools:$MINC_BIN_DIR:$PATH"
# MCRIBS (required legacy python)
COPY --from=nipreps/mcribs@sha256:d5ea7616402cbc0b80f32634832dce540a32bb1d5e1e61dfdd2cc795dba8944a /opt/MCRIBS/ /opt/MCRIBS
COPY --from=pyenv /usr/local/lib/ /usr/local/lib/
ENV PATH="/opt/MCRIBS/bin:/opt/MCRIBS/MIRTK/MIRTK-install/bin:/opt/MCRIBS/MIRTK/MIRTK-install/lib/tools:${PATH}" \
LD_LIBRARY_PATH="/opt/MCRIBS/lib:/opt/MCRIBS/ITK/ITK-install/lib:/opt/MCRIBS/VTK/VTK-install/lib:/opt/MCRIBS/MIRTK/MIRTK-install/lib:/usr/local/lib:${LD_LIBRARY_PATH}" \
MCRIBS_HOME="/opt/MCRIBS" \
PYTHONPATH="/opt/MCRIBS/lib/python:$PYTHONPATH"
# Create a shared $HOME directory
RUN useradd -m -s /bin/bash -G users nibabies && chmod -R 777 /home/nibabies
WORKDIR /home/nibabies
ENV HOME="/home/nibabies" \
LD_LIBRARY_PATH="/usr/lib/x86_64-linux-gnu:${LD_LIBRARY_PATH}"
COPY --from=micromamba /bin/micromamba /bin/micromamba
COPY --from=micromamba /opt/conda/envs/nibabies /opt/conda/envs/nibabies
ENV MAMBA_ROOT_PREFIX="/opt/conda"
RUN micromamba shell init -s bash && \
echo "micromamba activate nibabies" >> $HOME/.bashrc
ENV PATH="/opt/conda/envs/nibabies/bin:$PATH" \
CPATH="/opt/conda/envs/nibabies/include:$CPATH" \
LD_LIBRARY_PATH="/opt/conda/envs/nibabies/lib:$LD_LIBRARY_PATH" \
CONDA_PYTHON="/opt/conda/envs/nibabies/bin/python"
# FSL environment
ENV LANG="C.UTF-8" \
LC_ALL="C.UTF-8" \
PYTHONNOUSERSITE=1 \
FSLDIR="/opt/conda/envs/nibabies" \
FSLOUTPUTTYPE="NIFTI_GZ" \
FSLMULTIFILEQUIT="TRUE" \
FSLLOCKDIR="" \
FSLMACHINELIST="" \
FSLREMOTECALL="" \
FSLGECUDAQ="cuda.q"
# Unless otherwise specified each process should only use one thread - nipype
# will handle parallelization
ENV MKL_NUM_THREADS=1 \
OMP_NUM_THREADS=1 \
IS_DOCKER_8395080871=1
# Precaching atlases
COPY scripts/fetch_templates.py fetch_templates.py
RUN ${CONDA_PYTHON} -m pip install --no-cache-dir --upgrade templateflow && \
${CONDA_PYTHON} fetch_templates.py && \
rm fetch_templates.py && \
find $HOME/.cache/templateflow -type d -exec chmod go=u {} + && \
find $HOME/.cache/templateflow -type f -exec chmod go=u {} +
# Install pre-built wheel
COPY --from=src /src/dist/*.whl .
RUN ${CONDA_PYTHON} -m pip install --no-cache-dir $( ls *.whl )[telemetry,test]
# Facilitate Apptainer use
RUN find $HOME -type d -exec chmod go=u {} + && \
find $HOME -type f -exec chmod go=u {} + && \
rm -rf $HOME/.npm $HOME/.conda $HOME/.empty && \
ldconfig
WORKDIR /tmp
ARG BUILD_DATE
ARG VCS_REF
ARG VERSION
LABEL org.label-schema.build-date=$BUILD_DATE \
org.label-schema.name="NiBabies" \
org.label-schema.description="NiBabies - NeuroImaging tools for babies" \
org.label-schema.url="https://github.com/nipreps/nibabies" \
org.label-schema.vcs-ref=$VCS_REF \
org.label-schema.vcs-url="https://github.com/nipreps/nibabies" \
org.label-schema.version=$VERSION \
org.label-schema.schema-version="1.0"
ENTRYPOINT ["/opt/conda/envs/nibabies/bin/nibabies"]