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changelog.txt
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changelog.txt
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#########################
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