-
Notifications
You must be signed in to change notification settings - Fork 4
/
Copy pathchangelog.txt
236 lines (173 loc) · 8.33 KB
/
changelog.txt
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
#########################
4.1.3a
June 2020
########################
- R packages corpcor and Hotelling added
- python package dash upgraded to 1.12.0
- python package dash-bio upgraded to 0.4.8
- python package dash-core-components upgraded to 1.10.0
- python package dash-html-components upgraded to 1.0.3
- python package dash-table upgraded to 4.7.0
- KNIME upgraded to 4.1.3
- python KNIME plugin upgraded (4.1.3.v202005112253)
#########################
4.1.2a
April 2020
########################
- gtk2-engines-pixbuf installed into Ubuntu to remove some warning messages from the container run related to GTK
- autocutsel Ubuntu package removed and "autocutsel -fork" was removed from the xstartup
- r-recommended added to the R installation next to r-base and r-base-dev
- KNIME upgraded to 4.1.2
- python KNIME plugin upgraded
#########################
4.1.1a
March 2020
########################
- scripts for reset of Metanodes and Workflows templates git repositories now checking for the repository folder and return error when not exists
- scripts for reset of Metanodes and Workflows templates git repositories no display message about the finished synchronization until hide manually
- scripts for container start were changed so the container has bigger /dev/shm folder (used e.g. by Firefox and was causing its crashing)
- RAM usage monitoring applet added onto the top panel
- TigerVNC server upgraded to 1.10.1
- KNIME upgraded to 4.1.1
- majority of the KNIME plugins were upgraded, see https://github.com/OmicsWorkflows/KNIME_docker_vnc#list-of-used-programs-and-extensions-and-the-respective-licences for more details
- python3 upgraded to 3.6.9
- python packages versions were separated for python2 and python3
-- it is expected that the python2 implementation will be dropped from the next versions
-- some environment based packaging system si planned for the next versions
- python packages are now installed using pip as a non-root user
- as this is major update, majority of the KNIME extensions and python/R packages were upgraded, see the list of used programs for more details on the current versions (https://github.com/OmicsWorkflows/KNIME_docker_vnc#list-of-used-programs-and-extensions-and-the-respective-licences)
- R upgraded to 3.6.2
- R package gprofiler2 added
#########################
3.7.2a
August 2019
########################
- scripts for reset of Metanodes and Workflows templates git repositories were corrected to point to the directories (e.g. ".../gitfolders/KNIME_workflows" instead of ".../gitfolders/KNIME_Workflows")
- scripts for container start were changed to remove automatically exited container
- Java installation disabled for testing the system performance and stability
- pandoc Ubuntu package added
- ncbi-blast+ Ubuntu package added
- KNIME upgraded to 3.7.2
- KNIME python extension upgraded to 3.7.2.v201904170931
- KNIME PIA extension upgraded to 1.3.11.v201907181152
- KNIME Expressions extension upgraded to 3.7.2.v201904170930
- matplotlib python package upgraded to 3.1.0
-- two versions of matplotlib will be installed, 3.1.0 for python3 and 2.2.4 for python2 to maintain backward compatibility
- numpy python package upgraded to 1.16.4
- pandas python package upgraded to 0.24.2
- pip python package upgraded to 19.2.1
- scipy python package upgraded to 1.2.2
- statsmodels python package upgraded to 0.10.1
- added extra Ubuntu CRAN repository for R having the latest versions (3.5 and 3.6)
- R version specified explicitly
- R 3.6.1 installed
- RServe package installed from different repository to get latest version (https://rforge.net/)
- BioConductor packages are now installed using BiocManager::install()
- R package remotes added to enable installation of packages e.g. from GitHub
- R package proDA added from GitHub
#########################
3.7.1a
March 2019
########################
- scripts for reset of Metanodes and Workflows templates git repositories were adjusted to show the start and end of the reset routine
- added configuration files for xfce so one does not have to setup panels manually
- few additional system components installed because of plotly
- KNIME upgraded to 3.7.1 including R (3.7.1.v201901291055) and Python (3.7.1.v201901281201) extensions
- KNIME PIA extension upgraded to 1.3.10.v201903121258
- KNIME Expressions extension upgraded to 3.7.1.v201901281157
- pip python package upgraded to 19.0.3
- numpy python package upgraded to 1.16.2
- matplotlib python package upgraded to 3.0.3
- scipy python package upgraded to 1.2.1
- R package UpSetR added
- R package plotly added
#########################
3.7.0a
January 2019
########################
- xfce goodies were installed on top of xfce base desktop environment
- user group is now set together with the user
- Desktop shortcuts added to reset Metanodes and Workflows templates git repositories
- KNIME upgraded to 3.7.0 including R (3.7.0.v201810230750) and Python (3.7.0.v201812041252) extensions
- KNIME OpenMS extension upgraded to 2.4.0.201810261314
- KNIME PIA extension upgraded to 1.3.9.v201809131534
- KNIME Testing Framework extension added version 3.7.0.v201811021340
- KNIME Expressions extension added, version 3.7.0.v201811301633
- KNIME Report Designer extension added, version 3.7.0.v201808081048
- pip python package upgraded to 18.1
- numpy python package upgraded to 1.15.4
- scipy python package upgraded to 1.2.0
#########################
3.6.1a
8 September 2018
########################
- KNIME upgraded to 3.6.1
- KNIME python extension upgraded to 3.6.1.v201808311614
- KNIME r extension upgraded to 3.6.1.v201808311614
- pip python package upgraded to 18.0
- numpy python package upgraded to 1.15.1
- pandas python package upgraded to 0.23.4
- seaborn pytho package upgraded to 0.9.0
- matplotlib python package upgraded to 2.2.3
#########################
3.6.0x
10 August 2018
########################
- dockerfile based on Ubuntu 18.04
- KNIME 3.6.0 used
- R packages vsn and imp4p added
- upgraded numpy to 1.14.5 (newest version)
- upgraded pandas to 0.23.3 (newest version)
- removed byobu terminal
- added mc basic ubuntu package
- switched to xfce desktop environment due to better user experience and less issues with building the image/container
- knime_python_extension updated to 3.6.0.v201807061638
- tigervncserver is no longer installed - just unpacked (there is no prepared installation file for ubuntu 18.04 yet)
- tigervncserver updated to 1.9.0
- need to set user's login shell with chsh (otherwise terminal would cause bugs in 18.04)
- installing R...installing specific version no longer works
(R installed now using only 'apt-get install r-base' which is ok, but doesn't give control over the R version installed - which then affects bioclite packages version because they depend on R version)
#########################
3.5.3c
11th June 2018
########################
-added Biobase package to R via biocLite()
-dockerfile made cleaner - removed commented code about freefilesync + custom knime nodes
-removed knime update site "...community-contributions/trunk" because it might contain experimental versions of extensions
-downgraded openms to 2.3.0.201712211252 because experimental version was in use
-changed default Xmx to 4g for knime in knime.ini (max available memory)
-upgraded pandas to 0.23.0 (newest version)
-upgraded statsmodels to 0.9.0 (newest version)
-upgraded scipy to 1.1.0
-reorganized pip commands so that pip --upgade pip goes first + added setuptools + other packages are now installed in one install command
(this helps if networking problem - updated pip cca 9.0.1 is more robust than ubuntu 16.04 default pip (cca 8.1.1) if networking problems, retrying if exception)
##########################
3.5.3b
15th May 2018
##########################
-changed name of knime workspace folder to "knime-workspace"
it is because from now on, preferred way is to expose only one remote knime workspace folder to user
(previously he could acces al the workspaces)
###########################
3.5.3
4th May 2018
##########################
-initial release
from ubuntu:16.04
knime: 3.5.3
knime repositories version: 3.5
knime extensions:
-python: 3.5.2.v201802051356
-r: 3.5.1.v201712211140
-openms: 2.3.0.201804252103
-pia: 1.3.7.v201803061425
tigervnc: tigervncserver_1.8.0-1ubuntu1_amd64.deb
pip packages:
-pip: 9.0.3
-numpy: 1.14.3
-pandas: 0.22.0
-seaborn: 0.8.1
-statsmodels: 0.8.0
-matplotlib: 2.2.2
-scipy: 1.0.1
r:3.4.4-1xenial0