-
Notifications
You must be signed in to change notification settings - Fork 5
/
Dockerfile
350 lines (307 loc) · 11.3 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
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
FROM ubuntu:16.04
MAINTAINER Alexandre Savio <alexsavio@gmail.com>
RUN ln -snf /bin/bash /bin/sh
ARG DEBIAN_FRONTEND=noninteractive
ENV PETPVC_VERSION v1.2.1
ENV PETPVC_GIT https://github.com/UCL/PETPVC.git
ENV ITK_VERSION v4.12.2
ENV ITK_GIT http://itk.org/ITK.git
ENV VTK_VERSION v6.3.0
ENV VTK_GIT https://gitlab.kitware.com/vtk/vtk.git
ENV SIMPLEITK_VERSION v1.0.1
ENV SIMPLEITK_GIT http://itk.org/SimpleITK.git
ENV ANTS_VERSION v2.2.0
ENV ANTS_GIT https://github.com/stnava/ANTs.git
# ENV DCM2NIIX_VERSION v1.0.20171017
# ENV DCM2NIIX_GIT https://github.com/neurolabusc/dcm2niix.git
ENV NEURODEBIAN_URL http://neuro.debian.net/lists/xenial.de-m.full
ENV NEURODEBIAN_PGP hkp://pool.sks-keyservers.net:80 0xA5D32F012649A5A9
#ENV NEURODEBIAN_URL http://neuro.debian.net/lists/jessie.de-m.full
ENV LIBXP_URL http://mirrors.kernel.org/ubuntu/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb
ENV AFNI_URL https://afni.nimh.nih.gov/pub/dist/bin/linux_fedora_21_64/@update.afni.binaries
ENV CAMINO_GIT git://git.code.sf.net/p/camino/code
ENV SPM12_URL http://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/dev/spm12_latest_Linux_R2017b.zip
ENV MLAB_URL http://ssd.mathworks.com/supportfiles/downloads/R2017b/deployment_files/R2017b/installers/glnxa64/MCR_R2017b_glnxa64_installer.zip
ENV MCR_VERSION_DIR v93
ENV PYENV_NAME pyenv
ENV N_CPUS 2
## Configure default locale
# utils for local testing
# ENV() { export $1=$2; }; COPY() { cp -rdv $1 $2; };
RUN apt-get update && \
apt-get -y install apt-utils locales && \
echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen && \
locale-gen en_US.utf8 && \
/usr/sbin/update-locale LANG=en_US.UTF-8
# Set environment
ENV LC_ALL en_US.UTF-8
ENV LANG en_US.UTF-8
ENV LANGUAGE en_US.UTF-8
ENV TERM xterm
ENV HOME /work
ENV SOFT $HOME/soft
ENV BASHRC $HOME/.bashrc
# Create a non-priviledge user that will run the services
ENV BASICUSER basicuser
ENV BASICUSER_UID 1000
RUN useradd -m -d $HOME -s /bin/bash -N -u $BASICUSER_UID $BASICUSER && \
mkdir $SOFT && \
mkdir $HOME/.scripts && \
mkdir $HOME/.nipype
USER $BASICUSER
WORKDIR $HOME
# Add files.
COPY root/.* $HOME/
COPY root/* $HOME/
COPY root/.scripts/* $HOME/.scripts/
COPY root/.nipype/* $HOME/.nipype/
# neurodebian and Install.
USER root
RUN \
chown -R $BASICUSER $HOME && \
echo "export SOFT=\$HOME/soft" >> $BASHRC && \
echo "source /etc/fsl/5.0/fsl.sh" >> $BASHRC && \
echo "export FSLPARALLEL=condor" >> $BASHRC && \
apt-get update && \
apt-get install -y wget bzip2 unzip htop curl git && \
wget -O- $NEURODEBIAN_URL | tee /etc/apt/sources.list.d/neurodebian.sources.list && \
apt-key adv --recv-keys --keyserver hkp://pool.sks-keyservers.net:80 0xA5D32F012649A5A9 && \
sed -i 's/# \(.*multiverse$\)/\1/g' /etc/apt/sources.list && \
echo 'deb-src http://archive.ubuntu.com/ubuntu xenial main restricted' | tee /etc/apt/sources.list && \
apt-get update && \
apt-get -y upgrade && \
apt-get install -y \
apt-utils \
locales \
cmake \
gcc-4.9 \
g++-4.9 \
gfortran-4.9 \
gcc-5 \
g++-5 \
gfortran-5 \
tcsh \
libjpeg62 \
libxml2-dev \
libxslt1-dev \
dicomnifti \
dcm2niix \
xdot \
fsl-5.0-eddy-nonfree \
fsl-5.0-core && \
rm -rf /var/lib/apt/lists/* && \
update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-5 90 --slave /usr/bin/g++ g++ /usr/bin/g++-5 && \
update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.9 80 --slave /usr/bin/g++ g++ /usr/bin/g++-4.9 && \
apt-get build-dep vtk6
# && ln -s /usr/lib/x86_64-linux-gnu/libgsl.so /usr/lib/libgsl.so.0 && \
# Set the locale
RUN sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen && \
locale-gen
# #-------------------------------------------------------------------------------
# # DCM2NIIX
# #-------------------------------------------------------------------------------
# WORKDIR $SOFT
# RUN \
# mkdir dcm2niix && \
# cd dcm2niix && \
# git clone $DCM2NIIX_GIT -b $DCM2NIIX_VERSION DCM2NIIX && \
# mkdir build && \
# cd build && \
# cmake -DCMAKE_BUILD_TYPE=Release \
# ../DCM2NIIX && \
# make -j $N_CPUS && \
# make install && \
# cd ../.. && \
# rm -rf dcm2niix
#-------------------------------------------------------------------------------
# VTK (http://www.vtk.org)
#-------------------------------------------------------------------------------
WORKDIR $SOFT
RUN \
mkdir vtk && \
cd vtk && \
git clone $VTK_GIT -b $VTK_VERSION VTK && \
mkdir build && \
cd build && \
cmake -DCMAKE_BUILD_TYPE=Release \
-DPYTHON_EXECUTABLE=/usr/bin/python2.7 \
-DPYTHON_INCLUDE_DIR=/usr/include/python2.7 \
-DPYTHON_INCLUDE_DIR=/usr/include/x86_64-linux-gnu/python2.7m \
-DPYTHON_LIBRARY=/usr/lib/x86_64-linux-gnu/libpython2.7m.so.1 \
../VTK && \
make -j $N_CPUS && \
make install
#-------------------------------------------------------------------------------
# AFNI
# https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/install_instructs/steps_linux_ubuntu.html#install-steps-linux-ubuntu
#-------------------------------------------------------------------------------
WORKDIR $SOFT
RUN \
wget -c $LIBXP_URL && \
dpkg -i `basename $LIBXP_URL` && \
apt-get install -f && \
curl -O $AFNI_URL && \
chsh -s /usr/bin/tcsh && \
tcsh @update.afni.binaries -package linux_openmp_64 -do_extras && \
chsh -s /bin/bash && \
cp $HOME/abin/AFNI.afnirc $HOME/.afnirc && \
echo "addpath \$HOME/abin" >> $BASHRC && \
chown -R $BASICUSER $HOME/abin
#-------------------------------------------------------------------------------
## Here start the libraries that won't be installed in /usr/local
USER $BASICUSER
#-------------------------------------------------------------------------------
# ITK
#-------------------------------------------------------------------------------
# WORKDIR $SOFT
# RUN \
# mkdir itk && \
# cd itk && \
# git clone $ITK_GIT -b $ITK_VERSION && \
# mkdir build && \
# cd build && \
# cmake -DCMAKE_BUILD_TYPE=Release \
# -DPYTHON_EXECUTABLE=/usr/bin/python2.7 \
# -DPYTHON_INCLUDE_DIR=/usr/include/python2.7 \
# -DPYTHON_INCLUDE_DIR=/usr/include/x86_64-linux-gnu/python2.7m \
# -DPYTHON_LIBRARY=/usr/lib/x86_64-linux-gnu/libpython2.7m.so.1 \
# ../ITK && \
# make -j $N_CPUS && \
# make install && \
# echo "addpath \$SOFT/itk/build/bin" >> $BASHRC
# RUN ldconfig
#-------------------------------------------------------------------------------
# SimpleITK
#-------------------------------------------------------------------------------
# WORKDIR $SOFT
# RUN \
# mkdir simpleitk && \
# cd simpleitk && \
# git clone --recursive $SIMPLEITK_GIT -b $SIMPLEITK_VERSION && \
# mkdir build && \
# cd build && \
# cmake -DCMAKE_BUILD_TYPE=Release \
# -DPYTHON_EXECUTABLE=/usr/bin/python3 \
# -DPYTHON_INCLUDE_DIR=/usr/include/python3.5 \
# -DPYTHON_INCLUDE_DIR=/usr/include/x86_64-linux-gnu/python3.5m \
# -DPYTHON_LIBRARY=/usr/lib/x86_64-linux-gnu/libpython3.5m.so.1 \
# -DWRAP_JAVA=OFF \
# -DWRAP_CSHARP=OFF \
# -DWRAP_RUBY=OFF \
# ../SimpleITK/SuperBuild && \
# make -j $N_CPUS && \
# echo "addlibpath \$SOFT/simpleitk/build/lib" >> $BASHRC
#-------------------------------------------------------------------------------
# ANTS (https://github.com/stnava/ANTs)
#-------------------------------------------------------------------------------
WORKDIR $SOFT
RUN \
mkdir ants && \
cd ants && \
git clone $ANTS_GIT -b $ANTS_VERSION ANTs && \
mkdir build && \
cd build && \
cmake -DCMAKE_BUILD_TYPE=Release \
-DUSE_VTK=ON \
-DUSE_SYSTEM_VTK=ON \
-DVTK_DIR=$SOFT/vtk/build \
../ANTs && \
make -j $N_CPUS && \
echo "export ANTSPATH=\${SOFT}/ants/build/bin" >> $BASHRC && \
echo 'addpath \$ANTSPATH' >> $BASHRC
#-------------------------------------------------------------------------------
# PETPVC (https://github.com/UCL/PETPVC)
#-------------------------------------------------------------------------------
WORKDIR $SOFT
RUN \
mkdir petpvc && \
cd petpvc && \
git clone $PETPVC_GIT -b $PETPVC_VERSION && \
mkdir build && \
cd build && \
cmake -DCMAKE_BUILD_TYPE=Release \
-DITK_DIR=$SOFT/ants/build/ITKv4-build \
../PETPVC && \
make -j $N_CPUS && \
echo "addpath \${SOFT}/petpvc/build/src" >> $BASHRC
#-------------------------------------------------------------------------------
# Camino (http://camino.cs.ucl.ac.uk/)
#-------------------------------------------------------------------------------
#-------------------------------------------------------------------------------
# FSL (http://fsl.fmrib.ox.ac.uk)
#-------------------------------------------------------------------------------
WORKDIR $SOFT
RUN \
git clone $CAMINO_GIT camino && \
echo "addpath \${SOFT}/camino/bin" >> $BASHRC
#-------------------------------------------------------------------------------
# MATLAB and toolboxes
#-------------------------------------------------------------------------------
ENV MCR_DIR $SOFT/mcr
WORKDIR $SOFT
RUN \
echo "destinationFolder=$MCR_DIR" > mcr_options.txt && \
echo "agreeToLicense=yes" >> mcr_options.txt && \
echo "outputFile=/tmp/matlabinstall_log" >> mcr_options.txt && \
echo "mode=silent" >> mcr_options.txt && \
mkdir -p matlab_installer && \
curl -sSL $MLAB_URL -o matlab_installer/installer.zip && \
unzip matlab_installer/installer.zip -d matlab_installer/ && \
matlab_installer/install -inputFile mcr_options.txt && \
rm -rf matlab_installer mcr_options.txt && \
echo "export MCR_DIR=\$SOFT/mcr/\$MCR_VERSION_DIR" >> $BASHRC && \
echo "addpath \$MCR_DIR/bin" >> $BASHRC && \
cd $SOFT && \
curl -sSL $SPM12_URL -o spm12.zip && \
unzip spm12.zip && \
rm -rf spm12.zip && \
echo "export SPM_DIR=\$SOFT/spm12" >> $BASHRC && \
echo "export SPMMCRCMD='\$SPM_DIR/run_spm12.sh \$MCR_DIR script'" >> $BASHRC && \
echo "export FORCE_SPMMCR=1" >> $BASHRC
#-------------------------------------------------------------------------------
# Python environment with virtualenvwrapper
#-------------------------------------------------------------------------------
# Install Python 3 from miniconda
ENV PATH="$HOME/miniconda/bin:$PATH"
WORKDIR $SOFT
RUN \
wget -O miniconda.sh \
https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
bash miniconda.sh -b -p $HOME/miniconda && \
rm miniconda.sh && \
echo "addpath \$HOME/miniconda/bin" >> $BASHRC && \
conda update -y python conda && \
conda config --add channels conda-forge && \
conda install -y --no-deps \
matplotlib \
cycler \
freetype \
libpng \
pyparsing \
pytz \
python-dateutil \
six \
pip \
setuptools \
cython \
numpy \
scipy \
pandas \
scipy \
scikit-learn \
scikit-image \
statsmodels \
networkx \
pillow \
openblas \
&& conda clean -tipsy
# Install the other requirements
RUN pip install -r $HOME/requirements.txt && \
rm -rf ~/.cache/pip/ && \
source $BASHRC
#-------------------------------------------------------------------------------
# source .bashrc
#-------------------------------------------------------------------------------
USER root
RUN ldconfig
CMD ["/bin/bash"]