Contribute usegalaxy BE as instance where workflows can be successfully ran

[B0r1sD]

Hi GTN maintainers

At usegalaxy.be, we're making a stride to have all tools (and versions) that are being used in all GTN workflow files ('*.ga') installed in our instance. This is currently ongoing and 200+ additional tools have already been installed since (currently under the default 'Tools from workflows' section).

The main goal would be that every GTN tutorial can be ran on our instance, with certainty that it will run successfully. We see this as a win-win situation for both GTN and the Belgian instance; hope you do too!

We will need some help in the shape of a list of what we should do to make this possible. We are planning to automate this tool installation, checking the GTN codebase weekly for new or updated *.ga files as seen on the main branch.

If that is there, the ideal end result would be having usegalaxy.be as option underneath the 'Available on these Galaxies', under the label 'Known working'. Of course with the highest garantee we can get that it actually runs without troubles. So if this involves some kind of CI/CD or any other automation, we definitely want this set up with us or with you in this repo. We will need some guidance on where and how exactly we could contribute this ourselves.

Example image of dropdown I'm referring to:

In parallel, we have been running tool tests of every tool we have installed to fix/hide the ones that fail to minimize tool failures on our instance, which would also benefit this rigoroussness we are looking for.

Thank you in advance!
Team usegalaxy.be

[shiltemann]

@B0r1sD that is great to hear! the dropdown should update automatically, and is based on instances having all the tools and exact versions matching those in the workflows associated with the tutorial.

If you feel *.be should be in this list for certain tutorials but is not, please let me know and I will check up on this.

What this list does not capture, is whether any interactive tools used in the tutorial (and not part of the workflow) are available, or whether reference data needed by tools are available on your Galaxy, so this would be a more manual curation step, or when workflow tests are available you could run those periodically as well to flag any potential issues (but not all tutorial workflows come with tests yet)

[B0r1sD]

Ok thanks for the info @shiltemann, after all the tools are installed I'll take a look if I can indeed find BE in the dropdown of more tutorials! I'll get back to this issue when this has been completed.

We'll also put it in our list to update (and keep up-to-date) our Data Library for training material, which currently is not (https://usegalaxy.be/libraries/folders/F71dd6a15eadf6281/page/1).

[shiltemann]

@B0r1sD Just in case it is helpful, at the bottom of each tutorial we have a box with some code to install all tools required to support a tutorial based on a json file we autogenerate, e.g.:

you could iterate over all topics and tutorials to install all tools for the whole GTN (or we can autogenerate json files per topic for you orso)

Secondly, once you have installed tools and you think you should be listed in the dropdown but are not, check out the maintainer page of the topic, e.g. https://training.galaxyproject.org/training-material/topics/single-cell/maintainer.html and scroll down to "Topic Materials" and click the button in "Server compatibility" column, this should list each tool for a tutorial and whether it is installed on a Galaxy instance or not, so that you can see which tools are deemed missing.

[B0r1sD]

That maintainer page is a very handy resource, thanks for pointing it out! This will make this issue much easier to solve 👍 .