-
Notifications
You must be signed in to change notification settings - Fork 444
/
Dockerfile
1180 lines (1080 loc) · 48.4 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
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
FROM ubuntu:20.04
USER root
### BASICS ###
# Technical Environment Variables
ENV \
SHELL="/bin/bash" \
HOME="/root" \
# Nobteook server user: https://github.com/jupyter/docker-stacks/blob/master/base-notebook/Dockerfile#L33
NB_USER="root" \
USER_GID=0 \
XDG_CACHE_HOME="/root/.cache/" \
XDG_RUNTIME_DIR="/tmp" \
DISPLAY=":1" \
TERM="xterm" \
DEBIAN_FRONTEND="noninteractive" \
RESOURCES_PATH="/resources" \
SSL_RESOURCES_PATH="/resources/ssl" \
WORKSPACE_HOME="/workspace"
WORKDIR $HOME
# Make folders
RUN \
mkdir $RESOURCES_PATH && chmod a+rwx $RESOURCES_PATH && \
mkdir $WORKSPACE_HOME && chmod a+rwx $WORKSPACE_HOME && \
mkdir $SSL_RESOURCES_PATH && chmod a+rwx $SSL_RESOURCES_PATH
# Layer cleanup script
COPY resources/scripts/clean-layer.sh /usr/bin/clean-layer.sh
COPY resources/scripts/fix-permissions.sh /usr/bin/fix-permissions.sh
# Make clean-layer and fix-permissions executable
RUN \
chmod a+rwx /usr/bin/clean-layer.sh && \
chmod a+rwx /usr/bin/fix-permissions.sh
# Generate and Set locals
# https://stackoverflow.com/questions/28405902/how-to-set-the-locale-inside-a-debian-ubuntu-docker-container#38553499
RUN \
apt-get update && \
apt-get install -y locales && \
# install locales-all?
sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen && \
locale-gen && \
dpkg-reconfigure --frontend=noninteractive locales && \
update-locale LANG=en_US.UTF-8 && \
# Cleanup
clean-layer.sh
ENV LC_ALL="en_US.UTF-8" \
LANG="en_US.UTF-8" \
LANGUAGE="en_US:en"
# Install basics
RUN \
# TODO add repos?
# add-apt-repository ppa:apt-fast/stable
# add-apt-repository 'deb http://security.ubuntu.com/ubuntu xenial-security main'
apt-get update --fix-missing && \
apt-get install -y sudo apt-utils && \
apt-get upgrade -y && \
apt-get update && \
apt-get install -y --no-install-recommends \
# This is necessary for apt to access HTTPS sources:
apt-transport-https \
gnupg-agent \
gpg-agent \
gnupg2 \
ca-certificates \
build-essential \
pkg-config \
software-properties-common \
lsof \
net-tools \
libcurl4 \
curl \
wget \
cron \
openssl \
iproute2 \
psmisc \
tmux \
dpkg-sig \
uuid-dev \
csh \
xclip \
clinfo \
time \
libssl-dev \
libgdbm-dev \
libncurses5-dev \
libncursesw5-dev \
# required by pyenv
libreadline-dev \
libedit-dev \
xz-utils \
gawk \
# Simplified Wrapper and Interface Generator (5.8MB) - required by lots of py-libs
swig \
# Graphviz (graph visualization software) (4MB)
graphviz libgraphviz-dev \
# Terminal multiplexer
screen \
# Editor
nano \
# Find files
locate \
# Dev Tools
sqlite3 \
# XML Utils
xmlstarlet \
# GNU parallel
parallel \
# R*-tree implementation - Required for earthpy, geoviews (3MB)
libspatialindex-dev \
# Search text and binary files
yara \
# Minimalistic C client for Redis
libhiredis-dev \
# postgresql client
libpq-dev \
# mysql client (10MB)
libmysqlclient-dev \
# mariadb client (7MB)
# libmariadbclient-dev \
# image processing library (6MB), required for tesseract
libleptonica-dev \
# GEOS library (3MB)
libgeos-dev \
# style sheet preprocessor
less \
# Print dir tree
tree \
# Bash autocompletion functionality
bash-completion \
# ping support
iputils-ping \
# Map remote ports to localhosM
socat \
# Json Processor
jq \
rsync \
# sqlite3 driver - required for pyenv
libsqlite3-dev \
# VCS:
git \
subversion \
jed \
# odbc drivers
unixodbc unixodbc-dev \
# Image support
libtiff-dev \
libjpeg-dev \
libpng-dev \
libglib2.0-0 \
libxext6 \
libsm6 \
libxext-dev \
libxrender1 \
libzmq3-dev \
# protobuffer support
protobuf-compiler \
libprotobuf-dev \
libprotoc-dev \
autoconf \
automake \
libtool \
cmake \
fonts-liberation \
google-perftools \
# Compression Libs
# also install rar/unrar? but both are propriatory or unar (40MB)
zip \
gzip \
unzip \
bzip2 \
lzop \
# deprecates bsdtar (https://ubuntu.pkgs.org/20.04/ubuntu-universe-i386/libarchive-tools_3.4.0-2ubuntu1_i386.deb.html)
libarchive-tools \
zlibc \
# unpack (almost) everything with one command
unp \
libbz2-dev \
liblzma-dev \
zlib1g-dev && \
# Update git to newest version
add-apt-repository -y ppa:git-core/ppa && \
apt-get update && \
apt-get install -y --no-install-recommends git && \
# Fix all execution permissions
chmod -R a+rwx /usr/local/bin/ && \
# configure dynamic linker run-time bindings
ldconfig && \
# Fix permissions
fix-permissions.sh $HOME && \
# Cleanup
clean-layer.sh
# Add tini
RUN wget --no-verbose https://github.com/krallin/tini/releases/download/v0.19.0/tini -O /tini && \
chmod +x /tini
# prepare ssh for inter-container communication for remote python kernel
RUN \
apt-get update && \
apt-get install -y --no-install-recommends \
openssh-client \
openssh-server \
# SSLH for SSH + HTTP(s) Multiplexing
sslh \
# SSH Tooling
autossh \
mussh && \
chmod go-w $HOME && \
mkdir -p $HOME/.ssh/ && \
# create empty config file if not exists
touch $HOME/.ssh/config && \
sudo chown -R $NB_USER:users $HOME/.ssh && \
chmod 700 $HOME/.ssh && \
printenv >> $HOME/.ssh/environment && \
chmod -R a+rwx /usr/local/bin/ && \
# Fix permissions
fix-permissions.sh $HOME && \
# Cleanup
clean-layer.sh
RUN \
OPEN_RESTY_VERSION="1.19.3.2" && \
mkdir $RESOURCES_PATH"/openresty" && \
cd $RESOURCES_PATH"/openresty" && \
apt-get update && \
apt-get purge -y nginx nginx-common && \
# libpcre required, otherwise you get a 'the HTTP rewrite module requires the PCRE library' error
# Install apache2-utils to generate user:password file for nginx.
apt-get install -y libssl-dev libpcre3 libpcre3-dev apache2-utils && \
wget --no-verbose https://openresty.org/download/openresty-$OPEN_RESTY_VERSION.tar.gz -O ./openresty.tar.gz && \
tar xfz ./openresty.tar.gz && \
rm ./openresty.tar.gz && \
cd ./openresty-$OPEN_RESTY_VERSION/ && \
# Surpress output - if there is a problem remove > /dev/null
./configure --with-http_stub_status_module --with-http_sub_module > /dev/null && \
make -j2 > /dev/null && \
make install > /dev/null && \
# create log dir and file - otherwise openresty will throw an error
mkdir -p /var/log/nginx/ && \
touch /var/log/nginx/upstream.log && \
cd $RESOURCES_PATH && \
rm -r $RESOURCES_PATH"/openresty" && \
# Fix permissions
chmod -R a+rwx $RESOURCES_PATH && \
# Cleanup
clean-layer.sh
ENV PATH=/usr/local/openresty/nginx/sbin:$PATH
COPY resources/nginx/lua-extensions /etc/nginx/nginx_plugins
### END BASICS ###
### RUNTIMES ###
# Install Miniconda: https://repo.continuum.io/miniconda/
ENV \
# TODO: CONDA_DIR is deprecated and should be removed in the future
CONDA_DIR=/opt/conda \
CONDA_ROOT=/opt/conda \
PYTHON_VERSION="3.8.10" \
CONDA_PYTHON_DIR=/opt/conda/lib/python3.8 \
MINICONDA_VERSION=4.9.2 \
MINICONDA_MD5=122c8c9beb51e124ab32a0fa6426c656 \
CONDA_VERSION=4.9.2
RUN wget --no-verbose https://repo.anaconda.com/miniconda/Miniconda3-py38_${CONDA_VERSION}-Linux-x86_64.sh -O ~/miniconda.sh && \
echo "${MINICONDA_MD5} *miniconda.sh" | md5sum -c - && \
/bin/bash ~/miniconda.sh -b -p $CONDA_ROOT && \
export PATH=$CONDA_ROOT/bin:$PATH && \
rm ~/miniconda.sh && \
# Configure conda
# TODO: Add conde-forge as main channel -> remove if testted
# TODO, use condarc file
$CONDA_ROOT/bin/conda config --system --add channels conda-forge && \
$CONDA_ROOT/bin/conda config --system --set auto_update_conda False && \
$CONDA_ROOT/bin/conda config --system --set show_channel_urls True && \
$CONDA_ROOT/bin/conda config --system --set channel_priority strict && \
# Deactivate pip interoperability (currently default), otherwise conda tries to uninstall pip packages
$CONDA_ROOT/bin/conda config --system --set pip_interop_enabled false && \
# Update conda
$CONDA_ROOT/bin/conda update -y -n base -c defaults conda && \
$CONDA_ROOT/bin/conda update -y setuptools && \
$CONDA_ROOT/bin/conda install -y conda-build && \
# Update selected packages - install python 3.8.x
$CONDA_ROOT/bin/conda install -y --update-all python=$PYTHON_VERSION && \
# Link Conda
ln -s $CONDA_ROOT/bin/python /usr/local/bin/python && \
ln -s $CONDA_ROOT/bin/conda /usr/bin/conda && \
# Update
$CONDA_ROOT/bin/conda install -y pip && \
$CONDA_ROOT/bin/pip install --upgrade pip && \
chmod -R a+rwx /usr/local/bin/ && \
# Cleanup - Remove all here since conda is not in path as of now
# find /opt/conda/ -follow -type f -name '*.a' -delete && \
# find /opt/conda/ -follow -type f -name '*.js.map' -delete && \
$CONDA_ROOT/bin/conda clean -y --packages && \
$CONDA_ROOT/bin/conda clean -y -a -f && \
$CONDA_ROOT/bin/conda build purge-all && \
# Fix permissions
fix-permissions.sh $CONDA_ROOT && \
clean-layer.sh
ENV PATH=$CONDA_ROOT/bin:$PATH
# There is nothing added yet to LD_LIBRARY_PATH, so we can overwrite
ENV LD_LIBRARY_PATH=$CONDA_ROOT/lib
# Install pyenv to allow dynamic creation of python versions
RUN git clone https://github.com/pyenv/pyenv.git $RESOURCES_PATH/.pyenv && \
# Install pyenv plugins based on pyenv installer
git clone https://github.com/pyenv/pyenv-virtualenv.git $RESOURCES_PATH/.pyenv/plugins/pyenv-virtualenv && \
git clone git://github.com/pyenv/pyenv-doctor.git $RESOURCES_PATH/.pyenv/plugins/pyenv-doctor && \
git clone https://github.com/pyenv/pyenv-update.git $RESOURCES_PATH/.pyenv/plugins/pyenv-update && \
git clone https://github.com/pyenv/pyenv-which-ext.git $RESOURCES_PATH/.pyenv/plugins/pyenv-which-ext && \
apt-get update && \
# TODO: lib might contain high vulnerability
# Required by pyenv
apt-get install -y --no-install-recommends libffi-dev && \
clean-layer.sh
# Add pyenv to path
ENV PATH=$RESOURCES_PATH/.pyenv/shims:$RESOURCES_PATH/.pyenv/bin:$PATH \
PYENV_ROOT=$RESOURCES_PATH/.pyenv
# Install pipx
RUN pip install pipx && \
# Configure pipx
python -m pipx ensurepath && \
# Cleanup
clean-layer.sh
ENV PATH=$HOME/.local/bin:$PATH
# Install node.js
RUN \
apt-get update && \
# https://nodejs.org/en/about/releases/ use even numbered releases, i.e. LTS versions
curl -sL https://deb.nodesource.com/setup_14.x | sudo -E bash - && \
apt-get install -y nodejs && \
# As conda is first in path, the commands 'node' and 'npm' reference to the version of conda.
# Replace those versions with the newly installed versions of node
rm -f /opt/conda/bin/node && ln -s /usr/bin/node /opt/conda/bin/node && \
rm -f /opt/conda/bin/npm && ln -s /usr/bin/npm /opt/conda/bin/npm && \
# Fix permissions
chmod a+rwx /usr/bin/node && \
chmod a+rwx /usr/bin/npm && \
# Fix node versions - put into own dir and before conda:
mkdir -p /opt/node/bin && \
ln -s /usr/bin/node /opt/node/bin/node && \
ln -s /usr/bin/npm /opt/node/bin/npm && \
# Update npm
/usr/bin/npm install -g npm && \
# Install Yarn
/usr/bin/npm install -g yarn && \
# Install typescript
/usr/bin/npm install -g typescript && \
# Install webpack - 32 MB
/usr/bin/npm install -g webpack && \
# Install node-gyp
/usr/bin/npm install -g node-gyp && \
# Update all packages to latest version
/usr/bin/npm update -g && \
# Cleanup
clean-layer.sh
ENV PATH=/opt/node/bin:$PATH
# Java - removed
### END RUNTIMES ###
### PROCESS TOOLS ###
# Removed XRDP
# Install supervisor for process supervision
RUN \
apt-get update && \
# Create sshd run directory - required for starting process via supervisor
mkdir -p /var/run/sshd && chmod 400 /var/run/sshd && \
# Install rsyslog for syslog logging
apt-get install -y --no-install-recommends rsyslog && \
pipx install supervisor && \
pipx inject supervisor supervisor-stdout && \
# supervisor needs this logging path
mkdir -p /var/log/supervisor/ && \
# Cleanup
clean-layer.sh
### END PROCESS TOOLS ###
### GUI TOOLS ###
# Install xfce4 & gui tools
RUN \
# Use staging channel to get newest xfce4 version (4.16)
add-apt-repository -y ppa:xubuntu-dev/staging && \
apt-get update && \
apt-get install -y --no-install-recommends xfce4 && \
apt-get install -y --no-install-recommends gconf2 && \
apt-get install -y --no-install-recommends xfce4-terminal && \
apt-get install -y --no-install-recommends xfce4-clipman && \
apt-get install -y --no-install-recommends xterm && \
apt-get install -y --no-install-recommends --allow-unauthenticated xfce4-taskmanager && \
# Install dependencies to enable vncserver
apt-get install -y --no-install-recommends xauth xinit dbus-x11 && \
# Install gdebi deb installer
apt-get install -y --no-install-recommends gdebi && \
# Search for files
apt-get install -y --no-install-recommends catfish && \
apt-get install -y --no-install-recommends font-manager && \
# vs support for thunar
apt-get install -y thunar-vcs-plugin && \
# Streaming text editor for large files - klogg is alternative to glogg
apt-get install -y --no-install-recommends libqt5concurrent5 libqt5widgets5 libqt5xml5 && \
wget --no-verbose https://github.com/variar/klogg/releases/download/v20.12/klogg-20.12.0.813-Linux.deb -O $RESOURCES_PATH/klogg.deb && \
dpkg -i $RESOURCES_PATH/klogg.deb && \
rm $RESOURCES_PATH/klogg.deb && \
# Disk Usage Visualizer
apt-get install -y --no-install-recommends baobab && \
# Lightweight text editor
apt-get install -y --no-install-recommends mousepad && \
apt-get install -y --no-install-recommends vim && \
# Process monitoring
apt-get install -y --no-install-recommends htop && \
# Install Archive/Compression Tools: https://wiki.ubuntuusers.de/Archivmanager/
apt-get install -y p7zip p7zip-rar && \
apt-get install -y --no-install-recommends thunar-archive-plugin && \
apt-get install -y xarchiver && \
# DB Utils
apt-get install -y --no-install-recommends sqlitebrowser && \
# Install nautilus and support for sftp mounting
apt-get install -y --no-install-recommends nautilus gvfs-backends && \
# Install gigolo - Access remote systems
apt-get install -y --no-install-recommends gigolo gvfs-bin && \
# xfce systemload panel plugin - needs to be activated
# apt-get install -y --no-install-recommends xfce4-systemload-plugin && \
# Leightweight ftp client that supports sftp, http, ...
apt-get install -y --no-install-recommends gftp && \
# Install chrome
# sudo add-apt-repository ppa:system76/pop
add-apt-repository ppa:saiarcot895/chromium-beta && \
apt-get update && \
apt-get install -y chromium-browser chromium-browser-l10n chromium-codecs-ffmpeg && \
ln -s /usr/bin/chromium-browser /usr/bin/google-chrome && \
# Cleanup
apt-get purge -y pm-utils xscreensaver* && \
# Large package: gnome-user-guide 50MB app-install-data 50MB
apt-get remove -y app-install-data gnome-user-guide && \
clean-layer.sh
# Add the defaults from /lib/x86_64-linux-gnu, otherwise lots of no version errors
# cannot be added above otherwise there are errors in the installation of the gui tools
# Call order: https://unix.stackexchange.com/questions/367600/what-is-the-order-that-linuxs-dynamic-linker-searches-paths-in
ENV LD_LIBRARY_PATH=/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:$CONDA_ROOT/lib
# Install VNC
RUN \
apt-get update && \
# required for websockify
# apt-get install -y python-numpy && \
cd ${RESOURCES_PATH} && \
# Tiger VNC
wget -qO- https://sourceforge.net/projects/tigervnc/files/stable/1.11.0/tigervnc-1.11.0.x86_64.tar.gz/download | tar xz --strip 1 -C / && \
# Install websockify
mkdir -p ./novnc/utils/websockify && \
# Before updating the noVNC version, we need to make sure that our monkey patching scripts still work!!
wget -qO- https://github.com/novnc/noVNC/archive/v1.2.0.tar.gz | tar xz --strip 1 -C ./novnc && \
wget -qO- https://github.com/novnc/websockify/archive/v0.9.0.tar.gz | tar xz --strip 1 -C ./novnc/utils/websockify && \
chmod +x -v ./novnc/utils/*.sh && \
# create user vnc directory
mkdir -p $HOME/.vnc && \
# Fix permissions
fix-permissions.sh ${RESOURCES_PATH} && \
# Cleanup
clean-layer.sh
# Install Web Tools - Offered via Jupyter Tooling Plugin
## VS Code Server: https://github.com/codercom/code-server
COPY resources/tools/vs-code-server.sh $RESOURCES_PATH/tools/vs-code-server.sh
RUN \
/bin/bash $RESOURCES_PATH/tools/vs-code-server.sh --install && \
# Cleanup
clean-layer.sh
## ungit
COPY resources/tools/ungit.sh $RESOURCES_PATH/tools/ungit.sh
RUN \
/bin/bash $RESOURCES_PATH/tools/ungit.sh --install && \
# Cleanup
clean-layer.sh
## netdata
COPY resources/tools/netdata.sh $RESOURCES_PATH/tools/netdata.sh
RUN \
/bin/bash $RESOURCES_PATH/tools/netdata.sh --install && \
# Cleanup
clean-layer.sh
## Glances webtool is installed in python section below via requirements.txt
## Filebrowser
COPY resources/tools/filebrowser.sh $RESOURCES_PATH/tools/filebrowser.sh
RUN \
/bin/bash $RESOURCES_PATH/tools/filebrowser.sh --install && \
# Cleanup
clean-layer.sh
ARG ARG_WORKSPACE_FLAVOR="full"
ENV WORKSPACE_FLAVOR=$ARG_WORKSPACE_FLAVOR
# Install Visual Studio Code
COPY resources/tools/vs-code-desktop.sh $RESOURCES_PATH/tools/vs-code-desktop.sh
RUN \
# If minimal flavor - do not install
if [ "$WORKSPACE_FLAVOR" = "minimal" ]; then \
exit 0 ; \
fi && \
/bin/bash $RESOURCES_PATH/tools/vs-code-desktop.sh --install && \
# Cleanup
clean-layer.sh
# Install Firefox
COPY resources/tools/firefox.sh $RESOURCES_PATH/tools/firefox.sh
RUN \
# If minimal flavor - do not install
if [ "$WORKSPACE_FLAVOR" = "minimal" ]; then \
exit 0 ; \
fi && \
/bin/bash $RESOURCES_PATH/tools/firefox.sh --install && \
# Cleanup
clean-layer.sh
### END GUI TOOLS ###
### DATA SCIENCE BASICS ###
## Python 3
# Data science libraries requirements
COPY resources/libraries ${RESOURCES_PATH}/libraries
### Install main data science libs
RUN \
# Link Conda - All python are linke to the conda instances
# Linking python 3 crashes conda -> cannot install anyting - remove instead
# ln -s -f $CONDA_ROOT/bin/python /usr/bin/python3 && \
# if removed -> cannot use add-apt-repository
# rm /usr/bin/python3 && \
# rm /usr/bin/python3.5
ln -s -f $CONDA_ROOT/bin/python /usr/bin/python && \
apt-get update && \
# upgrade pip
pip install --upgrade pip && \
# If minimal flavor - install
if [ "$WORKSPACE_FLAVOR" = "minimal" ]; then \
# Install nomkl - mkl needs lots of space
conda install -y --update-all 'python='$PYTHON_VERSION nomkl ; \
else \
# Install mkl for faster computations
conda install -y --update-all 'python='$PYTHON_VERSION mkl-service mkl ; \
fi && \
# Install some basics - required to run container
conda install -y --update-all \
'python='$PYTHON_VERSION \
'ipython=7.24.*' \
'notebook=6.4.*' \
'jupyterlab=3.0.*' \
# TODO: nbconvert 6.x makes problems with template_path
'nbconvert=5.6.*' \
# TODO: temp fix: yarl version 1.5 is required for lots of libraries.
'yarl==1.5.*' \
# TODO install scipy, numpy, sklearn, and numexpr via conda for mkl optimizaed versions: https://docs.anaconda.com/mkl-optimizations/
'scipy==1.7.*' \
'numpy==1.19.*' \
scikit-learn \
numexpr && \
# installed via apt-get and pip: protobuf \
# installed via apt-get: zlib && \
# Switch of channel priority, makes some trouble
conda config --system --set channel_priority false && \
# Install minimal pip requirements
pip install --no-cache-dir --upgrade --upgrade-strategy only-if-needed -r ${RESOURCES_PATH}/libraries/requirements-minimal.txt && \
# If minimal flavor - exit here
if [ "$WORKSPACE_FLAVOR" = "minimal" ]; then \
# Remove pandoc - package for markdown conversion - not needed
# TODO: conda remove -y --force pandoc && \
# Fix permissions
fix-permissions.sh $CONDA_ROOT && \
# Cleanup
clean-layer.sh && \
exit 0 ; \
fi && \
# OpenMPI support
apt-get install -y --no-install-recommends libopenmpi-dev openmpi-bin && \
conda install -y --freeze-installed \
'python='$PYTHON_VERSION \
boost \
mkl-include && \
# Install mkldnn
conda install -y --freeze-installed -c mingfeima mkldnn && \
# Install pytorch - cpu only
conda install -y -c pytorch "pytorch==1.9.*" cpuonly && \
# Install light pip requirements
pip install --no-cache-dir --upgrade --upgrade-strategy only-if-needed -r ${RESOURCES_PATH}/libraries/requirements-light.txt && \
# If light light flavor - exit here
if [ "$WORKSPACE_FLAVOR" = "light" ]; then \
# Fix permissions
fix-permissions.sh $CONDA_ROOT && \
# Cleanup
clean-layer.sh && \
exit 0 ; \
fi && \
# libartals == 40MB liblapack-dev == 20 MB
apt-get install -y --no-install-recommends liblapack-dev libatlas-base-dev libeigen3-dev libblas-dev && \
# pandoc -> installs libluajit -> problem for openresty
# HDF5 (19MB)
apt-get install -y --no-install-recommends libhdf5-dev && \
# TBB threading optimization
apt-get install -y --no-install-recommends libtbb-dev && \
# required for tesseract: 11MB - tesseract-ocr-dev?
apt-get install -y --no-install-recommends libtesseract-dev && \
pip install --no-cache-dir tesserocr && \
# TODO: installs tenserflow 2.4 - Required for tensorflow graphics (9MB)
apt-get install -y --no-install-recommends libopenexr-dev && \
#pip install --no-cache-dir tensorflow-graphics==2020.5.20 && \
# GCC OpenMP (GOMP) support library
apt-get install -y --no-install-recommends libgomp1 && \
# Install Intel(R) Compiler Runtime - numba optimization
# TODO: don't install, results in memory error: conda install -y --freeze-installed -c numba icc_rt && \
# Install libjpeg turbo for speedup in image processing
conda install -y --freeze-installed libjpeg-turbo && \
# Add snakemake for workflow management
conda install -y -c bioconda -c conda-forge snakemake-minimal && \
# Add mamba as conda alternativ
conda install -y -c conda-forge mamba && \
# Faiss - A library for efficient similarity search and clustering of dense vectors.
conda install -y --freeze-installed faiss-cpu && \
# Install full pip requirements
pip install --no-cache-dir --upgrade --upgrade-strategy only-if-needed --use-deprecated=legacy-resolver -r ${RESOURCES_PATH}/libraries/requirements-full.txt && \
# Setup Spacy
# Spacy - download and large language removal
python -m spacy download en && \
# Fix permissions
fix-permissions.sh $CONDA_ROOT && \
# Cleanup
clean-layer.sh
# Fix conda version
RUN \
# Conda installs wrong node version - relink conda node to the actual node
rm -f /opt/conda/bin/node && ln -s /usr/bin/node /opt/conda/bin/node && \
rm -f /opt/conda/bin/npm && ln -s /usr/bin/npm /opt/conda/bin/npm
### END DATA SCIENCE BASICS ###
### JUPYTER ###
COPY \
resources/jupyter/start.sh \
resources/jupyter/start-notebook.sh \
resources/jupyter/start-singleuser.sh \
/usr/local/bin/
# Configure Jupyter / JupyterLab
# Add as jupyter system configuration
COPY resources/jupyter/nbconfig /etc/jupyter/nbconfig
COPY resources/jupyter/jupyter_notebook_config.json /etc/jupyter/
# install jupyter extensions
RUN \
# Create empty notebook configuration
mkdir -p $HOME/.jupyter/nbconfig/ && \
printf "{\"load_extensions\": {}}" > $HOME/.jupyter/nbconfig/notebook.json && \
# Activate and configure extensions
jupyter contrib nbextension install --sys-prefix && \
# nbextensions configurator
jupyter nbextensions_configurator enable --sys-prefix && \
# Configure nbdime
nbdime config-git --enable --global && \
# Activate Jupytext
jupyter nbextension enable --py jupytext --sys-prefix && \
# Enable useful extensions
jupyter nbextension enable skip-traceback/main --sys-prefix && \
# jupyter nbextension enable comment-uncomment/main && \
jupyter nbextension enable toc2/main --sys-prefix && \
jupyter nbextension enable execute_time/ExecuteTime --sys-prefix && \
jupyter nbextension enable collapsible_headings/main --sys-prefix && \
jupyter nbextension enable codefolding/main --sys-prefix && \
# Disable pydeck extension, cannot be loaded (404)
jupyter nbextension disable pydeck/extension && \
# Install and activate Jupyter Tensorboard
pip install --no-cache-dir git+https://github.com/InfuseAI/jupyter_tensorboard.git && \
jupyter tensorboard enable --sys-prefix && \
# TODO moved to configuration files = resources/jupyter/nbconfig Edit notebook config
# echo '{"nbext_hide_incompat": false}' > $HOME/.jupyter/nbconfig/common.json && \
cat $HOME/.jupyter/nbconfig/notebook.json | jq '.toc2={"moveMenuLeft": false,"widenNotebook": false,"skip_h1_title": false,"sideBar": true,"number_sections": false,"collapse_to_match_collapsible_headings": true}' > tmp.$$.json && mv tmp.$$.json $HOME/.jupyter/nbconfig/notebook.json && \
# If minimal flavor - exit here
if [ "$WORKSPACE_FLAVOR" = "minimal" ]; then \
# Cleanup
clean-layer.sh && \
exit 0 ; \
fi && \
# TODO: Not installed. Disable Jupyter Server Proxy
# jupyter nbextension disable jupyter_server_proxy/tree --sys-prefix && \
# Install jupyter black
jupyter nbextension install https://github.com/drillan/jupyter-black/archive/master.zip --sys-prefix && \
jupyter nbextension enable jupyter-black-master/jupyter-black --sys-prefix && \
# If light flavor - exit here
if [ "$WORKSPACE_FLAVOR" = "light" ]; then \
# Cleanup
clean-layer.sh && \
exit 0 ; \
fi && \
# Install and activate what if tool
pip install witwidget && \
jupyter nbextension install --py --symlink --sys-prefix witwidget && \
jupyter nbextension enable --py --sys-prefix witwidget && \
# Activate qgrid
jupyter nbextension enable --py --sys-prefix qgrid && \
# TODO: Activate Colab support
# jupyter serverextension enable --py jupyter_http_over_ws && \
# Activate Voila Rendering
# currently not working jupyter serverextension enable voila --sys-prefix && \
# Enable ipclusters
ipcluster nbextension enable && \
# Fix permissions? fix-permissions.sh $CONDA_ROOT && \
# Cleanup
clean-layer.sh
# install jupyterlab
RUN \
# without es6-promise some extension builds fail
npm install -g es6-promise && \
# define alias command for jupyterlab extension installs with log prints to stdout
jupyter lab build && \
lab_ext_install='jupyter labextension install -y --debug-log-path=/dev/stdout --log-level=WARN --minimize=False --no-build' && \
# jupyterlab installed in requirements section
$lab_ext_install @jupyter-widgets/jupyterlab-manager && \
# If minimal flavor - do not install jupyterlab extensions
if [ "$WORKSPACE_FLAVOR" = "minimal" ]; then \
# Final build with minimization
jupyter lab build -y --debug-log-path=/dev/stdout --log-level=WARN && \
# Cleanup
jupyter lab clean && \
jlpm cache clean && \
rm -rf $CONDA_ROOT/share/jupyter/lab/staging && \
clean-layer.sh && \
exit 0 ; \
fi && \
$lab_ext_install @jupyterlab/toc && \
# install temporarily from gitrepo due to the issue that jupyterlab_tensorboard does not work with 3.x yet as described here: https://github.com/chaoleili/jupyterlab_tensorboard/issues/28#issuecomment-783594541
#$lab_ext_install jupyterlab_tensorboard && \
pip install git+https://github.com/chaoleili/jupyterlab_tensorboard.git && \
# install jupyterlab git
# $lab_ext_install @jupyterlab/git && \
pip install jupyterlab-git && \
# jupyter serverextension enable --py jupyterlab_git && \
# For Matplotlib: https://github.com/matplotlib/jupyter-matplotlib
#$lab_ext_install jupyter-matplotlib && \
# Do not install any other jupyterlab extensions
if [ "$WORKSPACE_FLAVOR" = "light" ]; then \
# Final build with minimization
jupyter lab build -y --debug-log-path=/dev/stdout --log-level=WARN && \
# Cleanup
jupyter lab clean && \
jlpm cache clean && \
rm -rf $CONDA_ROOT/share/jupyter/lab/staging && \
clean-layer.sh && \
exit 0 ; \
fi \
# Install jupyterlab language server support
&& pip install jupyterlab-lsp==3.7.0 jupyter-lsp==1.3.0 && \
# $lab_ext_install install @krassowski/[email protected] && \
# For Plotly
$lab_ext_install jupyterlab-plotly && \
$lab_ext_install install @jupyter-widgets/jupyterlab-manager plotlywidget && \
# produces build error: jupyter labextension install jupyterlab-chart-editor && \
$lab_ext_install jupyterlab-chart-editor && \
# Install jupyterlab variable inspector - https://github.com/lckr/jupyterlab-variableInspector
pip install lckr-jupyterlab-variableinspector && \
# For holoview
# TODO: pyviz is not yet supported by the current JupyterLab version
# $lab_ext_install @pyviz/jupyterlab_pyviz && \
# Install Debugger in Jupyter Lab
# pip install --no-cache-dir xeus-python && \
# $lab_ext_install @jupyterlab/debugger && \
# Install jupyterlab code formattor - https://github.com/ryantam626/jupyterlab_code_formatter
$lab_ext_install @ryantam626/jupyterlab_code_formatter && \
pip install jupyterlab_code_formatter && \
jupyter serverextension enable --py jupyterlab_code_formatter \
# Final build with minimization
&& jupyter lab build -y --debug-log-path=/dev/stdout --log-level=WARN && \
jupyter lab build && \
# Cleanup
# Clean jupyter lab cache: https://github.com/jupyterlab/jupyterlab/issues/4930
jupyter lab clean && \
jlpm cache clean && \
# Remove build folder -> should be remove by lab clean as well?
rm -rf $CONDA_ROOT/share/jupyter/lab/staging && \
clean-layer.sh
# Install Jupyter Tooling Extension
COPY resources/jupyter/extensions $RESOURCES_PATH/jupyter-extensions
RUN \
pip install --no-cache-dir $RESOURCES_PATH/jupyter-extensions/tooling-extension/ && \
# Cleanup
clean-layer.sh
# Install and activate ZSH
COPY resources/tools/oh-my-zsh.sh $RESOURCES_PATH/tools/oh-my-zsh.sh
RUN \
# Install ZSH
/bin/bash $RESOURCES_PATH/tools/oh-my-zsh.sh --install && \
# Make zsh the default shell
# Initialize conda for command line activation
# TODO do not activate for now, opening the bash shell is a bit slow
# conda init bash && \
conda init zsh && \
chsh -s $(which zsh) $NB_USER && \
# Install sdkman - needs to be executed after zsh
curl -s https://get.sdkman.io | bash && \
# Cleanup
clean-layer.sh
# Install Git LFS
COPY resources/tools/git-lfs.sh $RESOURCES_PATH/tools/git-lfs.sh
RUN \
/bin/bash $RESOURCES_PATH/tools/git-lfs.sh --install && \
# Cleanup
clean-layer.sh
### VSCODE ###
# Install vscode extension
# https://github.com/cdr/code-server/issues/171
# Alternative install: /usr/local/bin/code-server --user-data-dir=$HOME/.config/Code/ --extensions-dir=$HOME/.vscode/extensions/ --install-extension ms-python-release && \
RUN \
SLEEP_TIMER=25 && \
# If minimal flavor -> exit here
if [ "$WORKSPACE_FLAVOR" = "minimal" ]; then \
exit 0 ; \
fi && \
cd $RESOURCES_PATH && \
mkdir -p $HOME/.vscode/extensions/ && \
# Install vs code jupyter - required by python extension
VS_JUPYTER_VERSION="2021.6.832593372" && \
wget --retry-on-http-error=429 --waitretry 15 --tries 5 --no-verbose https://marketplace.visualstudio.com/_apis/public/gallery/publishers/ms-toolsai/vsextensions/jupyter/$VS_JUPYTER_VERSION/vspackage -O ms-toolsai.jupyter-$VS_JUPYTER_VERSION.vsix && \
bsdtar -xf ms-toolsai.jupyter-$VS_JUPYTER_VERSION.vsix extension && \
rm ms-toolsai.jupyter-$VS_JUPYTER_VERSION.vsix && \
mv extension $HOME/.vscode/extensions/ms-toolsai.jupyter-$VS_JUPYTER_VERSION && \
sleep $SLEEP_TIMER && \
# Install python extension - (newer versions are 30MB bigger)
VS_PYTHON_VERSION="2021.5.926500501" && \
wget --no-verbose https://github.com/microsoft/vscode-python/releases/download/$VS_PYTHON_VERSION/ms-python-release.vsix && \
bsdtar -xf ms-python-release.vsix extension && \
rm ms-python-release.vsix && \
mv extension $HOME/.vscode/extensions/ms-python.python-$VS_PYTHON_VERSION && \
# && code-server --install-extension ms-python.python@$VS_PYTHON_VERSION \
sleep $SLEEP_TIMER && \
# If light flavor -> exit here
if [ "$WORKSPACE_FLAVOR" = "light" ]; then \
exit 0 ; \
fi && \
# Install prettie: https://github.com/prettier/prettier-vscode/releases
PRETTIER_VERSION="6.4.0" && \
wget --no-verbose https://github.com/prettier/prettier-vscode/releases/download/v$PRETTIER_VERSION/prettier-vscode-$PRETTIER_VERSION.vsix && \
bsdtar -xf prettier-vscode-$PRETTIER_VERSION.vsix extension && \
rm prettier-vscode-$PRETTIER_VERSION.vsix && \
mv extension $HOME/.vscode/extensions/prettier-vscode-$PRETTIER_VERSION.vsix && \
# Install code runner: https://github.com/formulahendry/vscode-code-runner/releases/latest
VS_CODE_RUNNER_VERSION="0.9.17" && \
wget --no-verbose https://github.com/formulahendry/vscode-code-runner/releases/download/$VS_CODE_RUNNER_VERSION/code-runner-$VS_CODE_RUNNER_VERSION.vsix && \
bsdtar -xf code-runner-$VS_CODE_RUNNER_VERSION.vsix extension && \
rm code-runner-$VS_CODE_RUNNER_VERSION.vsix && \
mv extension $HOME/.vscode/extensions/code-runner-$VS_CODE_RUNNER_VERSION && \
# && code-server --install-extension formulahendry.code-runner@$VS_CODE_RUNNER_VERSION \
sleep $SLEEP_TIMER && \
# Install ESLint extension: https://marketplace.visualstudio.com/items?itemName=dbaeumer.vscode-eslint
VS_ESLINT_VERSION="2.1.23" && \
wget --retry-on-http-error=429 --waitretry 15 --tries 5 --no-verbose https://marketplace.visualstudio.com/_apis/public/gallery/publishers/dbaeumer/vsextensions/vscode-eslint/$VS_ESLINT_VERSION/vspackage -O dbaeumer.vscode-eslint.vsix && \
# && wget --no-verbose https://github.com/microsoft/vscode-eslint/releases/download/$VS_ESLINT_VERSION-insider.2/vscode-eslint-$VS_ESLINT_VERSION.vsix -O dbaeumer.vscode-eslint.vsix && \
bsdtar -xf dbaeumer.vscode-eslint.vsix extension && \
rm dbaeumer.vscode-eslint.vsix && \
mv extension $HOME/.vscode/extensions/dbaeumer.vscode-eslint-$VS_ESLINT_VERSION.vsix && \
# && code-server --install-extension dbaeumer.vscode-eslint@$VS_ESLINT_VERSION \
# Fix permissions
fix-permissions.sh $HOME/.vscode/extensions/ && \
# Cleanup
clean-layer.sh
### END VSCODE ###
### INCUBATION ZONE ###
RUN \
apt-get update && \
# Required by magenta
# apt-get install -y libasound2-dev && \
# required by rodeo ide (8MB)
# apt-get install -y libgconf2-4 && \
# required for pvporcupine (800kb)
# apt-get install -y portaudio19-dev && \
# Audio drivers for magenta? (3MB)
# apt-get install -y libasound2-dev libjack-dev && \
# libproj-dev required for cartopy (15MB)
# apt-get install -y libproj-dev && \
# mysql server: 150MB
# apt-get install -y mysql-server && \
# If minimal or light flavor -> exit here
if [ "$WORKSPACE_FLAVOR" = "minimal" ] || [ "$WORKSPACE_FLAVOR" = "light" ]; then \
# Cleanup
clean-layer.sh && \
exit 0 ; \
fi && \
# Install fkill-cli program TODO: 30MB, remove?
# npm install --global fkill-cli && \
# Activate pretty-errors
# python -m pretty_errors -u -p && \
# Cleanup
clean-layer.sh
### END INCUBATION ZONE ###
### CONFIGURATION ###
# Copy files into workspace
COPY \
resources/docker-entrypoint.py \
resources/5xx.html \
$RESOURCES_PATH/
# Copy scripts into workspace
COPY resources/scripts $RESOURCES_PATH/scripts
# Create Desktop Icons for Tooling
COPY resources/branding $RESOURCES_PATH/branding
# Configure Home folder (e.g. xfce)
COPY resources/home/ $HOME/
# Copy some configuration files
COPY resources/ssh/ssh_config resources/ssh/sshd_config /etc/ssh/
COPY resources/nginx/nginx.conf /etc/nginx/nginx.conf
COPY resources/config/xrdp.ini /etc/xrdp/xrdp.ini
# Configure supervisor process
COPY resources/supervisor/supervisord.conf /etc/supervisor/supervisord.conf
# Copy all supervisor program definitions into workspace
COPY resources/supervisor/programs/ /etc/supervisor/conf.d/
# Assume yes to all apt commands, to avoid user confusion around stdin.
COPY resources/config/90assumeyes /etc/apt/apt.conf.d/
# Monkey Patching novnc: Styling and added clipboard support. All changed sections are marked with CUSTOM CODE
COPY resources/novnc/ $RESOURCES_PATH/novnc/
RUN \
## create index.html to forward automatically to `vnc.html`
# Needs to be run after patching
ln -s $RESOURCES_PATH/novnc/vnc.html $RESOURCES_PATH/novnc/index.html
# Basic VNC Settings - no password
ENV \
VNC_PW=vncpassword \
VNC_RESOLUTION=1600x900 \
VNC_COL_DEPTH=24
# Add tensorboard patch - use tensorboard jupyter plugin instead of the actual tensorboard magic
COPY resources/jupyter/tensorboard_notebook_patch.py $CONDA_PYTHON_DIR/site-packages/tensorboard/notebook.py
# Additional jupyter configuration
COPY resources/jupyter/jupyter_notebook_config.py /etc/jupyter/
COPY resources/jupyter/sidebar.jupyterlab-settings $HOME/.jupyter/lab/user-settings/@jupyterlab/application-extension/
COPY resources/jupyter/plugin.jupyterlab-settings $HOME/.jupyter/lab/user-settings/@jupyterlab/extensionmanager-extension/
COPY resources/jupyter/ipython_config.py /etc/ipython/ipython_config.py
# Branding of various components
RUN \
# Jupyter Branding
cp -f $RESOURCES_PATH/branding/logo.png $CONDA_PYTHON_DIR"/site-packages/notebook/static/base/images/logo.png" && \
cp -f $RESOURCES_PATH/branding/favicon.ico $CONDA_PYTHON_DIR"/site-packages/notebook/static/base/images/favicon.ico" && \
cp -f $RESOURCES_PATH/branding/favicon.ico $CONDA_PYTHON_DIR"/site-packages/notebook/static/favicon.ico" && \
# Fielbrowser Branding
mkdir -p $RESOURCES_PATH"/filebrowser/img/icons/" && \
cp -f $RESOURCES_PATH/branding/favicon.ico $RESOURCES_PATH"/filebrowser/img/icons/favicon.ico" && \
cp -f $RESOURCES_PATH/branding/favicon.ico $RESOURCES_PATH"/filebrowser/img/icons/favicon-32x32.png" && \