What is the recommended process for requesting that DeepTrio (the trio-aware extension of DeepVariant) be added as an available Galaxy tool? Specifically use galaxy org
DeepTrio is now widely used for germline trio WGS calling, with significantly improved de novo accuracy compared to single-sample DeepVariant. It is containerized and fits naturally alongside existing Galaxy tools (BWA-MEM, DeepVariant, GATK).
If community help is useful, what would be the best way to contribute — I have my doubts about my ability in this regard, but I’m willing to try?
Great! I’m not sure if the IUC is already planning to wrap this tool yet or not but they will usually help to support new development efforts by the community! Many tools are expanded and polished this way too. How this works is below!
Locating development information for existing tools
How to learn who authored an existing tool wrapper can be done a few ways.
The source tool (and dependencies) are usually available as a conda package.
I didn’t find DeepTrio in Bioconda yet or did I miss it? Adding new packages is pretty common, and benefits everyone (not just Galaxy!), so this can be resolved and might be a first step.
As you work through this, the IUC matrix chat is great for questions. Your PR is also a place for feedback. Sometimes we can help here, too – see tool-dev for prior topics.
Publishing
Once a tool is wrapped and published into the Main Tool Shed, it will flow out to all of the public Galaxy servers. Local server administrators will also be able to install for their users!
Training and Help
Teaching users how to use your tool is important!
Tool form
The tool form itself is valuable real estate that is directly in front on the user right when they have a question about the functionality or how an option is used. Advice is commonly given as tips inline with the options then additional context, short help, or Galaxy-specific usage is explained down in the Help section on tool forms.
GTN
You can also consider creating a GTN Tutorial for your tool! If the tool is supported by a publication with a use-case example, this could be simplified for the tutorial example. Be sure to see the tutorials we have to support the addition of new content!
IWC
Create a polished version of your workflow and publish it at the IWC https://iwc.galaxyproject.org/ InterGalactic Workflow Commission! This is our suite of HTP workflows that are also cross published over to Dockstore and Workflowhub. These are robust artifacts used by API users (not just web-based users).
User channels: Matrix, Help
Finally, consider being available at the Galaxy Matrix chat and here at this Help forum to offer users advice as they interact with your tool! Setting up a keyword ping is one way.
I’m glad you asked about this! New tool development is really important. The information hasn’t been gathered into a topic in 2026 yet so I took the opportunity to put it all together here.
I hope this provides some context but please let us know if it actually does. Follow up questions are welcome!
IWC 
