Docker Galaxy Stable Versions Save

• a lot of new Galaxy features (https://docs.galaxyproject.org/en/latest/releases/20.09_announce.html)

• a lot of new Galaxy features (https://docs.galaxyproject.org/en/latest/releases/20.05_announce.html)
• cleanups from @abretaud to the travis setup
• epic rework of the compose based setup, including new tests, new images, everything new by @AndreasSko

• This is featuring the latest and greatest from the Galaxy community

• Switch back to /bin/bash as default shell for galaxy user

• The image is now based on ubuntu:18.04 (instead of ubuntu:14.04 previously) and PostgreSQL 11.5 (9.3 previously). See migration documention to migrate the postgresql database from 9.3 to 11.5.
• We stopped supporting old Galaxy tool dependencies. If you have an old installation (/export directory) things will still work
• The compose version will not be useable during the 19.05 release as we have major refactoring to do. Please check out the 19.01 tag for the time being.

• This is featuring the latest and greatest from the Galaxy community
• Please note that this release will be the last release which is based on ubuntu:14.04 and PostgreSQL 9.3. We will migrate to ubuntu:18.04 and a newer PostgreSQL version in 19.05. Furthermore, we will not support old Galaxy tool dependencies.

Anthony Bretaudeau (@abretaud) added the following features to the startup script.

• update most of the config sample files during startup
• update the database (only if the new GALAXY_AUTO_UPDATE_DB is set)
• update all tools from the flavor yml list(s) (only if the path to yml file(s) is provided with the new GALAXY_AUTO_UPDATE_TOOLS var)
• update conda installed in /export/tool_deps (only if the new GALAXY_AUTO_UPDATE_CONDA is set)

• new and more powerful orchestration build script (build-orchestration-images.sh) by @pcm32
• a lot of bug-fixes to the compose setup by @abretaud
• and of course a great Galaxy release

All features from: https://docs.galaxyproject.org/en/master/releases/18.05_announce.html

General

• tracking the Galaxy release_18.01 branch
• uwsgi work to adopt to changes for 18.01
• remove nodejs-legacy & npm from Dockerfile and install latest version from ansible-extras
• initial galaxy.ini → galaxy.yml integration

Compose:

• grafana and influxdb container
• Galaxy telegraf integration to push to influxdb
• added some documentation