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@bgruening
bgruening authored Nov 12, 2024
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# Changelog

- 0.1: Initial release!
## 0.1: Initial release!
- with Apache2, PostgreSQL and Tool Shed integration
- 0.2: complete new Galaxy stack.
## 0.2: complete new Galaxy stack.
- with nginx, uwsgi, proftpd, docker, supervisord and SLURM
- 0.3: Add Interactive Environments
## 0.3: Add Interactive Environments
- IPython in docker in Galaxy in docker
- advanged logging
- 0.4:
## 0.4:
- base the image on toolshed/requirements with all required Galaxy dependencies
- use Ansible roles to build large parts of the image
- export the supervisord web interface on port 9002
- enable Galaxy reports webapp
- 15.07:
## 15.07:
- `install-biojs` can install BioJS visualisations into Galaxy
- `add-tool-shed` can be used to activate third party Tool Sheds in child Dockerfiles
- many documentation improvements
- RStudio is now part of Galaxy and this Image
- configurable postgres UID/GID by @chambm
- smarter starting of postgres during Tool installations by @shiltemann
- 15.10:
## 15.10:
- new Galaxy 15.10 release
- fix https://github.com/bgruening/docker-galaxy-stable/issues/94
- 16.01:
## 16.01:
- enable Travis testing for all builds and PR
- offer new [yaml based tool installations](https://github.com/galaxyproject/ansible-galaxy-tools/blob/master/files/tool_list.yaml.sample)
- enable dynamic UWSGI processes and threads with `-e UWSGI_PROCESSES=2` and `-e UWSGI_THREADS=4`
- enable dynamic Galaxy handlers `-e GALAXY_HANDLER_NUMPROCS=2`
- Addition of a new `lite` mode contributed by @kellrott
- first release with Jupyter integration
- 16.04:
## 16.04:
- include a Galaxy-bare mode, enable with `-e BARE=True`
- first release with [HTCondor](https://research.cs.wisc.edu/htcondor/) installed and pre-configured
- 16.07:
## 16.07:
- documentation and tests updates for SLURM integration by @mvdbeek
- first version with initial Docker compose support (proftpd ✔️)
- SFTP support by @zfrenchee
- 16.10:
## 16.10:
- [HTTPS support](https://github.com/bgruening/docker-galaxy-stable/pull/240 ) by @zfrenchee and @mvdbeek
- 17.01:
## 17.01:
- enable Conda dependency resolution by default
- [new Galaxy version](https://docs.galaxyproject.org/en/master/releases/17.01_announce.html)
- more compose work (slurm, postgresql)
- 17.05:
## 17.05:
- add PROXY_PREFIX variable to enable automatic configuration of Galaxy running under some prefix (@abretaud)
- enable quota by default (just the funtionality, not any specific value)
- HT-Condor is now supported in compose with semi-autoscaling and BioContainers
- Galaxy Docker Compose is completely under Travis testing and available with SLURM and HT-Condor
- using Docker `build-arg`s for GALAXY_RELEASE and GALAXY_REPO
- 17.09:
## 17.09:
- much improved documentation about using Galaxy Docker and an external cluster (@rhpvorderman)
- CVMFS support - mounting in 4TB of pre-build reference data (@chambm)
- Singularity support and tests (compose only)
- more work on K8s support and testing (@jmchilton)
- using .env files to configure the compose setup for SLURM, Condor, K8s, SLURM-Singularity, Condor-Docker
- 18.01:
## 18.01:
- 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
- grafana and influxdb container (compose)
- Galaxy telegraf integration to push to influxdb (compose)
- added some documentation (compose)
- 18.05:
## 18.05:
- Nothing very special, but a awesome Galaxy release as usual
- 18.09:
## 18.09:
- new and more powerful orchestration build script (build-orchestration-images.sh) by @pcm32
- a lot of bug-fixes to the compose setup by @abretaud
- 19.01:
## 19.01:
- 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.
- 19.05:
## 19.05:
- 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](#Postgresql-migration) to migrate the postgresql database from 9.3 to 11.5.
- We not longer support old Galaxy tool dependencies.
- 20.05:
## 20.05:
- Featuring Galaxy 20.05
- Completely reworked compose setup
- The default admin password and apikey (`GALAXY_DEFAULT_ADMIN_PASSWORD` and `GALAXY_DEFAULT_ADMIN_KEY`) have changed: the password is now `password` (instead of `admin`) and the apikey `fakekey` (instead of `admin`).
- 20.09:
## 20.09:
- Featuring Galaxy 20.09
- 24.1:
## 24.1:
- Deprecating the `compose` setup.
- Complete new setup, adjusting to the latest Galaxy stack.
- Base Ubuntu Image: Upgraded from version 18.04 to 22.04
Expand All @@ -98,29 +98,27 @@
- Flower: Added Flower service on port 5555 for monitoring and debugging Celery. The dashboard is exposed via Nginx and is available at the /flower/ path. The default access credentials are admin:admin.
- TUSd: Added TUSd server on port 1080 to support fault-tolerant uploads; Nginx is configured to proxy TUSd.
- gx-it-proxy: Added gx-it-proxy service on port 4002 to support Interactive Tools.

- Ansible Playbooks:
- Migrated from galaxyextras git submodule to using mainatined ansible roles.
- Added configure_rabbitmq_users.yml Ansible playbook, which removes the default guest user and adds admin, galaxy, and flower users for RabbitMQ during container startup.
- Environment Variables:
- Added `GUNICORN_WORKERS` and `CELERY_WORKERS` magic environment variables to set the number of Gunicorn and Celery workers, respectively, during container startup.

- Configuration Changes:
- Replaced the Galaxy Reports sample configuration file.
- Removed galaxy_web, handlers, reports, and ie_proxy services from Supervisor.
- Added Gravity for managing Galaxy services such as Gunicorn, Celery, gx-it-proxy, TUSd, reports, and handlers. It uses Supervisor as the process manager, with the configuration file located at /etc/galaxy/gravity.yml.
- Added support for dynamic handlers (set as the default handler type).
- Redis and Flower services are now managed by Supervisor.
- Since Galaxy Interactive Environments are deprecated, they have been replaced by Interactive Tools (ITs). The sample configuration file tools_conf_interactive.xml.sample is placed inside GALAXY_CONFIG_DIR. Nginx is also configured to support both domain and path-based ITs.
- Switched to using the cvmfs-config.galaxyproject.org repository for automatic configuration and updates of Galaxy project CVMFS repositories. Updated tool data table config path to include CVMFS locations from data.galaxyproject.org in --privileged mode.
- Enabled IPv6 support in Nginx for ports 80 and 443.
- Added Subject Alternative Name (SAN) extension (DNS:localhost and IP:127.0.0.1) while generating a self-signed SSL certificate.
- Ensured the Nginx SSL certificate is trusted system-wide by adding it to the CA store.
- Updated Galaxy extra dependencies.
- Added docker_net, docker_auto_rm, and docker_set_user parameters for Docker-enabled job destinations.
- Added update_yaml_value.py script to update nested key values in a YAML file.
- Replaced ie_proxy with gx-it-proxy.
- Replaced nginx_upload_module with TUSd for delegated uploads.
- CI Tests:
- Added dive tool for analyzing the docker image
- Added test for check data persistence
- Ansible Playbooks:
- Migrated from galaxyextras git submodule to using mainatined ansible roles.
- Added configure_rabbitmq_users.yml Ansible playbook, which removes the default guest user and adds admin, galaxy, and flower users for RabbitMQ during container startup.
- Environment Variables:
- Added `GUNICORN_WORKERS` and `CELERY_WORKERS` magic environment variables to set the number of Gunicorn and Celery workers, respectively, during container startup.
- Configuration Changes:
- Replaced the Galaxy Reports sample configuration file.
- Removed galaxy_web, handlers, reports, and ie_proxy services from Supervisor.
- Added Gravity for managing Galaxy services such as Gunicorn, Celery, gx-it-proxy, TUSd, reports, and handlers. It uses Supervisor as the process manager, with the configuration file located at /etc/galaxy/gravity.yml.
- Added support for dynamic handlers (set as the default handler type).
- Redis and Flower services are now managed by Supervisor.
- Since Galaxy Interactive Environments are deprecated, they have been replaced by Interactive Tools (ITs). The sample configuration file tools_conf_interactive.xml.sample is placed inside GALAXY_CONFIG_DIR. Nginx is also configured to support both domain and path-based ITs.
- Switched to using the cvmfs-config.galaxyproject.org repository for automatic configuration and updates of Galaxy project CVMFS repositories. Updated tool data table config path to include CVMFS locations from data.galaxyproject.org in --privileged mode.
- Enabled IPv6 support in Nginx for ports 80 and 443.
- Added Subject Alternative Name (SAN) extension (DNS:localhost and IP:127.0.0.1) while generating a self-signed SSL certificate.
- Ensured the Nginx SSL certificate is trusted system-wide by adding it to the CA store.
- Updated Galaxy extra dependencies.
- Added docker_net, docker_auto_rm, and docker_set_user parameters for Docker-enabled job destinations.
- Added update_yaml_value.py script to update nested key values in a YAML file.
- Replaced ie_proxy with gx-it-proxy.
- Replaced nginx_upload_module with TUSd for delegated uploads.
- CI Tests
- Added dive tool for analyzing the docker image
- Added test for check data persistence

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