/
Dockerfile
182 lines (161 loc) · 7.17 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
# Use Ubuntu 16.04 LTS
FROM ubuntu:xenial-20161213
# Pre-cache neurodebian key
COPY docker/files/neurodebian.gpg /usr/local/etc/neurodebian.gpg
# Installing Neurodebian packages (FSL, AFNI, git)
RUN apt-get update && \
apt-get install -y --no-install-recommends curl && \
apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* && \
curl -sSL "http://neuro.debian.net/lists/xenial.us-ca.full" >> /etc/apt/sources.list.d/neurodebian.sources.list && \
apt-key add /usr/local/etc/neurodebian.gpg && \
(apt-key adv --refresh-keys --keyserver hkp://ha.pool.sks-keyservers.net 0xA5D32F012649A5A9 || true)
# Prepare environment
RUN apt-get update && \
apt-get install -y --no-install-recommends \
autoconf \
build-essential \
bzip2 \
ca-certificates \
curl \
cython3 \
ed \
git \
git-annex-standalone \
graphviz=2.38.0-12ubuntu2 \
gsl-bin \
libglib2.0-0 \
libglu1-mesa-dev \
libglw1-mesa \
libgomp1 \
libjpeg62 \
libtool \
libxm4 \
netpbm \
pkg-config \
tcsh \
xfonts-base \
xvfb \
fsl-core=5.0.9-5~nd16.04+1 \
fsl-mni152-templates && \
curl -sSL https://deb.nodesource.com/setup_10.x | bash - && \
apt-get install -y --no-install-recommends \
nodejs && \
echo "Install libxp (not in all ubuntu/debian repositories)" && \
apt-get install -yq --no-install-recommends libxp6 \
|| /bin/bash -c " \
curl --retry 5 -o /tmp/libxp6.deb -sSL http://mirrors.kernel.org/debian/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb \
&& dpkg -i /tmp/libxp6.deb && rm -f /tmp/libxp6.deb" && \
echo "Install libpng12 (not in all ubuntu/debian repositories" && \
apt-get install -yq --no-install-recommends libpng12-0 \
|| /bin/bash -c " \
curl -o /tmp/libpng12.deb -sSL http://mirrors.kernel.org/debian/pool/main/libp/libpng/libpng12-0_1.2.49-1%2Bdeb7u2_amd64.deb \
&& dpkg -i /tmp/libpng12.deb && rm -f /tmp/libpng12.deb" && \
ln -s /usr/lib/x86_64-linux-gnu/libgsl.so.19 /usr/lib/x86_64-linux-gnu/libgsl.so.0 && \
ldconfig && \
apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
ENV FSLDIR="/usr/share/fsl/5.0" \
FSLOUTPUTTYPE="NIFTI_GZ" \
FSLMULTIFILEQUIT="TRUE" \
POSSUMDIR="/usr/share/fsl/5.0" \
LD_LIBRARY_PATH="/usr/lib/fsl/5.0:$LD_LIBRARY_PATH" \
FSLTCLSH="/usr/bin/tclsh" \
FSLWISH="/usr/bin/wish"
ENV PATH="/usr/lib/fsl/5.0:/usr/lib/afni/bin:$PATH"
# Installing ANTs 2.2.0 (NeuroDocker build)
ENV ANTSPATH=/usr/lib/ants
RUN mkdir -p $ANTSPATH && \
curl -sSL "https://dl.dropbox.com/s/2f4sui1z6lcgyek/ANTs-Linux-centos5_x86_64-v2.2.0-0740f91.tar.gz" \
| tar -xzC $ANTSPATH --strip-components 1
ENV PATH=$ANTSPATH:$PATH
# Installing AFNI (version 17_3_03 archived on OSF)
RUN mkdir -p /opt/afni && \
curl -o afni.tar.gz -sSLO "https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/5a0dd9a7b83f69027512a12b" && \
tar zxv -C /opt/afni --strip-components=1 -f afni.tar.gz && \
rm -rf afni.tar.gz
ENV PATH=/opt/afni:$PATH \
AFNI_MODELPATH="/opt/afni/models" \
AFNI_IMSAVE_WARNINGS="NO" \
AFNI_TTATLAS_DATASET="/opt/afni/atlases" \
AFNI_PLUGINPATH="/opt/afni/plugins"
# Create a shared $HOME directory
RUN useradd -m -s /bin/bash -G users bidsapp
WORKDIR /home/bidsapp
ENV HOME="/home/bidsapp"
# Installing SVGO
RUN npm install -g svgo
# Installing and setting up miniconda
RUN curl -sSLO https://repo.continuum.io/miniconda/Miniconda3-4.5.11-Linux-x86_64.sh && \
bash Miniconda3-4.5.11-Linux-x86_64.sh -b -p /usr/local/miniconda && \
rm Miniconda3-4.5.11-Linux-x86_64.sh
# Set CPATH for packages relying on compiled libs (e.g. indexed_gzip)
ENV PATH="/usr/local/miniconda/bin:$PATH" \
CPATH="/usr/local/miniconda/include/:$CPATH" \
LANG="C.UTF-8" \
LC_ALL="C.UTF-8" \
# PYTHONWARNINGS="ignore,default:::mriqc,default:::nipype" \
PYTHONNOUSERSITE=1
# Installing precomputed python packages
RUN conda install -y python=3.7.1 \
graphviz=2.40.1 \
libxml2=2.9.8 \
libxslt=1.1.32 \
matplotlib=2.2.2 \
mkl-service \
mkl=2018.0.3 \
numpy=1.15.4 \
pandas=0.23.4 \
scikit-learn=0.19.1 \
scipy=1.1.0 \
setuptools>=40.0.0 \
traits=4.6.0 \
pip=19.1 \
zlib; sync && \
chmod -R a+rX /usr/local/miniconda; sync && \
chmod +x /usr/local/miniconda/bin/*; sync && \
conda build purge-all; sync && \
conda clean -tipsy && sync
# Unless otherwise specified each process should only use one thread - nipype
# will handle parallelization
ENV MKL_NUM_THREADS=1 \
OMP_NUM_THREADS=1
# Precaching fonts, set 'Agg' as default backend for matplotlib
RUN python -c "from matplotlib import font_manager" && \
sed -i 's/\(backend *: \).*$/\1Agg/g' $( python -c "import matplotlib; print(matplotlib.matplotlib_fname())" )
# Installing dev requirements (packages that are not in pypi)
WORKDIR /src/
COPY requirements.txt requirements.txt
RUN pip install --no-cache-dir -r requirements.txt
# Precaching atlases
RUN python -c "from templateflow import api as tfapi; \
tfapi.get('MNI152NLin2009cAsym', resolution=[1, 2], suffix='T1w', desc=None); \
tfapi.get('MNI152NLin2009cAsym', resolution=[1, 2], suffix='mask',\
desc=['brain', 'head']); \
tfapi.get('MNI152NLin2009cAsym', resolution=1, suffix='dseg', desc='carpet'); \
tfapi.get('MNI152NLin2009cAsym', resolution=1, suffix='probseg',\
label=['CSF', 'GM', 'WM']);\
tfapi.get('MNI152NLin2009cAsym', resolution=[1, 2], suffix='boldref')"
# Installing MRIQC
COPY . /src/mriqc
ARG VERSION
# Force static versioning within container
RUN echo "${VERSION}" > /src/mriqc/mriqc/VERSION && \
echo "include mriqc/VERSION" >> /src/mriqc/MANIFEST.in && \
cd /src/mriqc && \
pip install --no-cache-dir .[all]
RUN find $HOME -type d -exec chmod go=u {} + && \
find $HOME -type f -exec chmod go=u {} +
# Best practices
RUN ldconfig
WORKDIR /tmp/
# Run mriqc by default
ENTRYPOINT ["/usr/local/miniconda/bin/mriqc"]
ARG BUILD_DATE
ARG VCS_REF
LABEL org.label-schema.build-date=$BUILD_DATE \
org.label-schema.name="MRIQC" \
org.label-schema.description="MRIQC - Automated Quality Control and visual reports for Quality Assesment of structural (T1w, T2w) and functional MRI of the brain" \
org.label-schema.url="http://mriqc.readthedocs.io" \
org.label-schema.vcs-ref=$VCS_REF \
org.label-schema.vcs-url="https://github.com/poldracklab/mriqc" \
org.label-schema.version=$VERSION \
org.label-schema.schema-version="1.0"