Dependency resolution with conda is now the default and recommended method for tool installation. Start here: https://docs.galaxyproject.org/en/latest/admin/dependency_resolvers.html && https://docs.galaxyproject.org/en/latest/admin/conda_faq.html
The versions of Galaxy noted are over a year old – use the latest versions of Galaxy releases for the best functionality. You’ll find that the dependency resolution functions are no longer in beta and can be customized. Using default settings is generally best unless you have specific reasons to install differently. The links above cover the options.
If you need help with a Docker version of Galaxy, this Gitter chat is a direct way to communicate with the image maintainers: https://gitter.im/bgruening/docker-galaxy-stable
The Galaxy Test ToolShed https://testtoolshed.g2.bx.psu.edu/ is a testing sandbox – meaning, tools are not in a stable/release form. Obtain tools from the Galaxy Main ToolShed https://toolshed.g2.bx.psu.edu/ instead.
If a tool is only available in the Test ToolShed, and not in the Main ToolShed, it may still be useable, but installation may not work “automatically” and require some advanced tuning. Explore the development repository for the tool (is usually linked to the tool’s ToolShed page, but not required, especially at the Test ToolShed), review open known issues, and open a new issue there describing problems as needed.
The tool wrapper authors are the best resource for troubleshooting installation issues (if using managed dependencies and the most current version of Galaxy itself). An exception can be tool wrappers authored by the IUC or Devteam – you can ask if there are known issues (if you can’t find one yet at the development repository) or for installation help (after reviewing the development docs linked above) at this Gitter chat: https://gitter.im/galaxy-iuc/iuc
Please be aware that some tools may no longer be actively maintained, and some may use older or custom dependency resolution methods. ToolSheds are community resources – anyone can publish a tool there. How to tell if a tool is maintained/functional or requires a specific installation method? 1) The tool wrapper’s publication date, how many times downloaded, and other notes on the tool’s ToolShed page and 2) commit/update dates at the linked development repository.
The Test and Main ToolSheds were just upgraded, so there were recently windows where tool installation was expected to not function correctly, no matter which ToolShed was the source. Example Q&A about that at this Gitter chat: https://gitter.im/galaxyproject/dev?at=5f59fa68a5788a3c29e651a5
Current and historical status/notes about downtime are at the Galaxy status page. It includes all usegalaxy.* servers and core resources like ToolSheds. https://galaxyproject.statuspage.io/
Hope that helps!