-
Notifications
You must be signed in to change notification settings - Fork 12
/
Dockerfile
393 lines (326 loc) · 14.6 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
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
FROM jupyter/base-notebook:2023-10-20
# https://hub.docker.com/r/jupyter/base-notebook/tags
# Parent image source
# https://github.com/jupyter/docker-stacks/blob/86d42cadf4695b8e6fc3b3ead58e1f71067b765b/docker-stacks-foundation/Dockerfile
# https://github.com/jupyter/docker-stacks/blob/86d42cadf4695b8e6fc3b3ead58e1f71067b765b/base-notebook/Dockerfile
LABEL maintainer="Neurodesk Project <www.neurodesk.org>"
USER root
#========================================#
# Core services
#========================================#
# Install base image dependencies
RUN apt-get update --yes \
&& DEBIAN_FRONTEND=noninteractive apt install --yes --no-install-recommends \
# Apptainer
software-properties-common \
# Apache Tomcat
openjdk-19-jre \
# Apache Guacamole
## Core
build-essential \
libcairo2-dev \
libjpeg-turbo8-dev \
libpng-dev \
libtool-bin \
uuid-dev \
## Optionals
freerdp2-dev \
libvncserver-dev \
libssl-dev \
libwebp-dev \
libssh2-1-dev \
strace \
# SSH (Optional)
libpango1.0-dev \
## VNC
tigervnc-common \
tigervnc-standalone-server \
tigervnc-tools \
## RDP
xorgxrdp \
xrdp \
# Desktop Env
lxde \
# Installer tools
acl \
wget \
curl \
dirmngr \
gpg \
gpg-agent \
software-properties-common \
apt-transport-https \
&& apt-get clean && rm -rf /var/lib/apt/lists/*
ARG TOMCAT_REL="9"
ARG TOMCAT_VERSION="9.0.87"
ARG GUACAMOLE_VERSION="1.5.5"
ENV LANG ""
ENV LANGUAGE ""
ENV LC_ALL ""
# Install apptainer
RUN add-apt-repository -y ppa:apptainer/ppa \
&& apt-get update --yes \
&& DEBIAN_FRONTEND=noninteractive apt-get install --yes apptainer \
&& apt-get clean && rm -rf /var/lib/apt/lists/* \
&& rm -rf /root/.cache && rm -rf /home/${NB_USER}/.cache
# Install Apache Tomcat
RUN wget -q https://archive.apache.org/dist/tomcat/tomcat-${TOMCAT_REL}/v${TOMCAT_VERSION}/bin/apache-tomcat-${TOMCAT_VERSION}.tar.gz -P /tmp \
&& tar -xf /tmp/apache-tomcat-${TOMCAT_VERSION}.tar.gz -C /tmp \
&& rm -rf /tmp/apache-tomcat-${TOMCAT_VERSION}.tar.gz \
&& mv /tmp/apache-tomcat-${TOMCAT_VERSION} /usr/local/tomcat \
&& mv /usr/local/tomcat/webapps /usr/local/tomcat/webapps.dist \
&& mkdir /usr/local/tomcat/webapps \
&& chmod +x /usr/local/tomcat/bin/*.sh
# Install Apache Guacamole
RUN wget -q "https://archive.apache.org/dist/guacamole/${GUACAMOLE_VERSION}/binary/guacamole-${GUACAMOLE_VERSION}.war" -O /usr/local/tomcat/webapps/ROOT.war \
&& wget -q "https://archive.apache.org/dist/guacamole/${GUACAMOLE_VERSION}/source/guacamole-server-${GUACAMOLE_VERSION}.tar.gz" -P /tmp \
&& tar xvf /tmp/guacamole-server-${GUACAMOLE_VERSION}.tar.gz -C /tmp \
&& rm /tmp/guacamole-server-${GUACAMOLE_VERSION}.tar.gz \
&& cd /tmp/guacamole-server-${GUACAMOLE_VERSION} \
&& ./configure --with-init-dir=/etc/init.d \
&& make \
&& make install \
&& ldconfig \
&& rm -r /tmp/guacamole-server-${GUACAMOLE_VERSION}
# Set home directory default acls
RUN chmod g+rwxs /home/${NB_USER}
RUN setfacl -dRm u::rwX,g::rwX,o::0 /home/${NB_USER}
# #========================================#
# # Software (as root user)
# #========================================#
# Add Software sources
RUN wget -qO- https://packages.microsoft.com/keys/microsoft.asc | gpg --dearmor > packages.microsoft.gpg \
&& install -D -o root -g root -m 644 packages.microsoft.gpg /etc/apt/keyrings/packages.microsoft.gpg \
&& sh -c 'echo "deb [arch=amd64,arm64,armhf signed-by=/etc/apt/keyrings/packages.microsoft.gpg] https://packages.microsoft.com/repos/code stable main" > /etc/apt/sources.list.d/vscode.list' \
&& rm -f packages.microsoft.gpg \
# Nextcloud Client
&& add-apt-repository ppa:nextcloud-devs/client \
&& chmod -R 770 /home/${NB_USER}/.launchpadlib \
&& chown -R ${NB_UID}:${NB_GID} /home/${NB_USER}/.launchpadlib \
# NodeJS
&& curl -fsSL https://deb.nodesource.com/setup_20.x | bash - \
&& apt-get clean && rm -rf /var/lib/apt/lists/*
# Install CVMFS
RUN wget -q https://ecsft.cern.ch/dist/cvmfs/cvmfs-release/cvmfs-release-latest_all.deb -P /tmp \
&& dpkg -i /tmp/cvmfs-release-latest_all.deb \
&& rm /tmp/cvmfs-release-latest_all.deb
# Install Tools and Libs
RUN apt-get update --yes \
&& DEBIAN_FRONTEND=noninteractive apt install --yes --no-install-recommends \
aria2 \
code \
cvmfs \
datalad \
davfs2 \
debootstrap \
emacs \
gedit \
git \
gnome-keyring \
graphviz \
htop \
imagemagick \
iputils-ping \
less \
libgfortran5 \
libgpgme-dev \
libossp-uuid-dev \
libpci3 \
libreoffice \
lmod \
lua-bit32 \
lua-filesystem \
lua-json \
lua-lpeg \
lua-posix \
lua-term \
lua5.2 \
lxtask \
man-db \
nano \
nextcloud-client \
nodejs \
openssh-client \
openssh-server \
owncloud-client \
pciutils \
qdirstat \
rsync \
s3fs \
screen \
sshfs \
tcllib \
tk \
tmux \
tree \
uidmap \
unzip \
vim \
xdg-utils \
yarn \
zip \
&& apt-get clean && rm -rf /var/lib/apt/lists/*
# Install firefox
RUN add-apt-repository ppa:mozillateam/ppa \
&& apt-get update --yes \
&& DEBIAN_FRONTEND=noninteractive apt install --yes --no-install-recommends \
--target-release 'o=LP-PPA-mozillateam' firefox \
&& apt-get clean && rm -rf /var/lib/apt/lists/*
COPY config/firefox/mozillateamppa /etc/apt/preferences.d/mozillateamppa
COPY config/firefox/syspref.js /etc/firefox/syspref.js
#========================================#
# Software (as notebook user)
#========================================#
USER ${NB_USER}
# Install conda packages
RUN conda install -c conda-forge nb_conda_kernels \
&& conda clean --all -f -y \
&& rm -rf /home/${NB_USER}/.cache
RUN conda config --system --prepend envs_dirs '~/conda-environments'
# Add datalad-container datalad-osf osfclient ipyniivue to the conda environment
RUN /opt/conda/bin/pip install nipype matplotlib datalad-container datalad-osf osfclient ipyniivue \
&& rm -rf /home/${NB_USER}/.cache
# Install jupyter-server-proxy and disable announcements
# Deprecated: jupyter labextension install ..
# jupyter_server_proxy needs to be at least 4.2.0 to fix CVE-2024-35225
RUN /opt/conda/bin/pip install jupyter-server-proxy \
&& /opt/conda/bin/jupyter labextension disable @jupyterlab/apputils-extension:announcements \
&& /opt/conda/bin/pip install jupyterlmod \
&& /opt/conda/bin/pip install jupyterlab-git \
&& /opt/conda/bin/pip install jupyterlab_rise \
&& /opt/conda/bin/pip install ipycanvas \
&& /opt/conda/bin/pip install jupyter-resource-usage \
&& /opt/conda/bin/pip install jupyter_scheduler \
&& /opt/conda/bin/pip install ipywidgets ipyvolume jupyterlab_widgets \
&& rm -rf /home/${NB_USER}/.cache
#========================================#
# Configuration (as root user)
#========================================#
USER root
# Create cvmfs keys
RUN mkdir -p /etc/cvmfs/keys/ardc.edu.au
COPY config/cvmfs/neurodesk.ardc.edu.au.pub /etc/cvmfs/keys/ardc.edu.au/neurodesk.ardc.edu.au.pub
COPY config/cvmfs/neurodesk.ardc.edu.au.conf /etc/cvmfs/config.d/neurodesk.ardc.edu.au.conf
COPY config/cvmfs/default.local /etc/cvmfs/default.local
# # Customise logo, wallpaper, terminal
COPY config/jupyter/neurodesk_brain_logo.svg /opt/neurodesk_brain_logo.svg
COPY config/jupyter/neurodesk_brain_icon.svg /opt/neurodesk_brain_icon.svg
COPY config/lxde/background.png /usr/share/lxde/wallpapers/desktop_wallpaper.png
COPY config/lxde/pcmanfm.conf /etc/xdg/pcmanfm/LXDE/pcmanfm.conf
COPY config/lxde/lxterminal.conf /usr/share/lxterminal/lxterminal.conf
COPY config/lmod/module.sh /usr/share/
# Configure tiling of windows SHIFT-ALT-CTR-{Left,right,top,Bottom} and other openbox desktop mods
COPY ./config/lxde/rc.xml /etc/xdg/openbox
# Allow the root user to access the sshfs mount
# https://github.com/NeuroDesk/neurodesk/issues/47
RUN sed -i 's/#user_allow_other/user_allow_other/g' /etc/fuse.conf
# Fetch singularity bind mount list and create placeholder mountpoints
# RUN mkdir -p `curl https://raw.githubusercontent.com/NeuroDesk/neurocontainers/master/recipes/globalMountPointList.txt`
# Fix "No session for pid prompt"
RUN rm /usr/bin/lxpolkit
# enable rootless mounts:
RUN chmod +x /usr/bin/fusermount
# Add notebook startup scripts
# https://jupyter-docker-stacks.readthedocs.io/en/latest/using/common.html
RUN mkdir -p /usr/local/bin/start-notebook.d/ \
&& mkdir -p /usr/local/bin/before-notebook.d/
COPY config/jupyter/start_notebook.sh /usr/local/bin/start-notebook.d/
COPY config/jupyter/before_notebook.sh /usr/local/bin/before-notebook.d/
# Add jupyter notebook and startup scripts for system-wide configuration
COPY --chown=root:users config/jupyter/jupyter_notebook_config.py /etc/jupyter/jupyter_notebook_config.py
COPY --chown=root:users config/jupyter/jupyterlab_startup.sh /opt/neurodesktop/jupyterlab_startup.sh
COPY --chown=root:users config/guacamole/guacamole.sh /opt/neurodesktop/guacamole.sh
COPY --chown=root:users config/jupyter/environment_variables.sh /opt/neurodesktop/environment_variables.sh
COPY --chown=root:users config/guacamole/user-mapping.xml /etc/guacamole/user-mapping.xml
RUN chmod +x /etc/jupyter/jupyter_notebook_config.py \
/opt/neurodesktop/jupyterlab_startup.sh \
/opt/neurodesktop/guacamole.sh \
/opt/neurodesktop/environment_variables.sh
# Create Guacamole configurations (user-mapping.xml gets filled in the startup.sh script)
RUN mkdir -p /etc/guacamole \
&& echo -e "user-mapping: /etc/guacamole/user-mapping.xml\nguacd-hostname: 127.0.0.1" > /etc/guacamole/guacamole.properties \
&& echo -e "[server]\nbind_host = 127.0.0.1\nbind_port = 4822" > /etc/guacamole/guacd.conf
# Add NB_USER to sudoers
RUN echo "${NB_USER} ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers.d/notebook \
# The following apply to Singleuser mode only. See config/jupyter/before_notebook.sh for Notebook mode
&& /usr/bin/printf '%s\n%s\n' 'password' 'password' | passwd ${NB_USER} \
&& usermod --shell /bin/bash ${NB_USER}
# Enable deletion of non-empty-directories in JupyterLab: https://github.com/jupyter/notebook/issues/4916
RUN sed -i 's/c.FileContentsManager.delete_to_trash = False/c.FileContentsManager.always_delete_dir = True/g' /etc/jupyter/jupyter_server_config.py
# Copy script to test_containers
COPY config/test_neurodesktop.sh /usr/share/test_neurodesktop.sh
# Install version 1.1.1 of fix_bash.sh that is required for test_containers
RUN chmod +x /usr/share/test_neurodesktop.sh \
&& git clone https://github.com/civier/fix_bash.git /tmp/fix_bash \
&& cd /tmp/fix_bash \
&& git checkout tags/1.1.1 \
&& cp /tmp/fix_bash/fix_bash.sh /usr/share \
&& rm -Rf /tmp/fix_bash
#========================================#
# Configuration (as notebook user)
#========================================#
# Switch to notebook user
USER ${NB_USER}
# Configure ITKsnap
RUN mkdir -p /home/${NB_USER}/.itksnap.org/ITK-SNAP \
&& chown ${NB_USER} /home/${NB_USER}/.itksnap.org -R
COPY --chown=${NB_UID}:${NB_GID} ./config/itksnap/UserPreferences.xml /home/${NB_USER}/.itksnap.org
COPY --chown=${NB_UID}:${NB_GID} ./config/lxde/mimeapps.list /home/${NB_USER}/.config/mimeapps.list
COPY --chown=${NB_UID}:${NB_GID} config/lxde/panel /home/${NB_USER}/.config/lxpanel/LXDE/panels/panel
COPY --chown=${NB_UID}:${NB_GID} config/lxde/.bashrc /home/${NB_USER}/tmp_bashrc
RUN cat /home/${NB_USER}/tmp_bashrc >> /home/${NB_USER}/.bashrc \
&& rm /home/${NB_USER}/tmp_bashrc
# Setup git
RUN git config --global user.email "[email protected]" \
&& git config --global user.name "Neurodesk User"
# Setup temp directory for matplotlib (required for fmriprep)
RUN mkdir -p /home/${NB_USER}/.config/matplotlib-mpldir \
&& chmod -R 700 /home/${NB_USER}/.config/matplotlib-mpldir \
&& chown -R ${NB_UID}:${NB_GID} /home/${NB_USER}/.config/matplotlib-mpldir
COPY --chown=${NB_UID}:${NB_GID} config/vscode/settings.json /home/${NB_USER}/.config/Code/User/settings.json
# Add libfm script
RUN mkdir -p /home/${NB_USER}/.config/libfm
COPY --chown=${NB_UID}:${NB_GID} ./config/lxde/libfm.conf /home/${NB_USER}/.config/libfm
RUN touch /home/${NB_USER}/.sudo_as_admin_successful
ENV DONT_PROMPT_WSL_INSTALL=1
ENV LMOD_CMD /usr/share/lmod/lmod/libexec/lmod
# Add startup and config files for neurodesktop, jupyter, guacamole, vnc
RUN mkdir /home/${NB_USER}/.vnc \
&& chown ${NB_USER} /home/${NB_USER}/.vnc \
&& /usr/bin/printf '%s\n%s\n%s\n' 'password' 'password' 'n' | vncpasswd
COPY --chown=${NB_UID}:${NB_GID} config/lxde/xstartup /home/${NB_USER}/.vnc
COPY --chown=${NB_UID}:${NB_GID} config/conda/conda-readme.md /home/${NB_USER}/
RUN mkdir -p /home/${NB_USER}/.ssh \
&& chmod -R 700 /home/${NB_USER}/.ssh \
&& setfacl -dRm u::rwx,g::0,o::0 /home/${NB_USER}/.ssh
COPY --chown=${NB_UID}:${NB_GID} config/ssh/sshd_config /home/${NB_USER}/.ssh/sshd_config
RUN chmod +x /home/${NB_USER}/.vnc/xstartup
# Set up working directories and symlinks
RUN mkdir -p /home/${NB_USER}/Desktop/
#========================================#
# Finalise build
#========================================#
# Switch to root user
USER root
# Save a backup copy of startup home dir into /tmp
# Used to restore home dir in persistent sessions
RUN cp -rp /home/${NB_USER} /tmp/
# Set up data directory so it exists in the container for the SINGULARITY_BINDPATH
RUN mkdir -p /data
# Install neurocommand
ADD "https://api.github.com/repos/neurodesk/neurocommand/git/refs/heads/main" /tmp/skipcache
RUN rm /tmp/skipcache \
&& git clone https://github.com/NeuroDesk/neurocommand.git /neurocommand \
&& cd /neurocommand \
&& bash build.sh --lxde --edit \
&& bash install.sh \
&& ln -s /home/${NB_USER}/neurodesktop-storage/containers /neurocommand/local/containers
USER ${NB_UID}
WORKDIR "${HOME}"
# Install example notebooks
ADD "https://api.github.com/repos/neurodesk/example-notebooks/git/refs/heads/main" /home/${NB_USER}/skipcache
RUN rm /home/${NB_USER}/skipcache \
&& git clone --depth 1 https://github.com/NeuroDesk/example-notebooks
# Set SINGULARITY_BINDPATH and MODULEPATH here so it's available within a notebook (the startup scripts set these things too late):
ENV APPTAINER_BINDPATH=/data,/mnt,/neurodesktop-storage,/tmp,/cvmfs
ENV MODULEPATH=/cvmfs/neurodesk.ardc.edu.au/containers/modules/