Add link to AIV reference history on Galaxy US

[wm75]

Also bumps tool versions used and adds a bit of explanation on how phylogenetic trees can be visualized in Galaxy.

Most importantly, this will enable people to follow the tutorial on usegalaxy.org in addition to Galaxy Europe.

Agreed that this is sort of a quick fix and that the data in question should really live on zenodo, but I'm still in the process of figuring out the final shape of this tutorial.

[bgruening]

There is a way to annotate this as metadata have you tried that?

[wm75]

For zenodo data I know that, but for shared histories?

[hexylena]

We should add an FAQ for it, but, yes, they can be annotated. e.g.

input_histories:
  - label: "UseGalaxy.eu"
    history: https://humancellatlas.usegalaxy.eu/u/wendi.bacon.training/h/cs1pre-processing-with-alevin---input-1
answer_histories:
  - label: "UseGalaxy.eu (includes AnnData to CDS conversion)"
    history: https://humancellatlas.usegalaxy.eu/u/j.jakiela/h/monoce3-tutorial-workflow
    date: 2024-03-04

[bgruening]

https://raw.githubusercontent.com/galaxyproject/training-material/refs/heads/main/topics/single-cell/tutorials/scrna-case_alevin/tutorial.md

[bgruening]

Question more to @davelopez. Should we make those histories archived, so Wolfgang can not delete them accidentally or add new stuff to it? How should we handle those histories in the long run.

[davelopez]

Question more to @davelopez. Should we make those histories archived, so Wolfgang can not delete them accidentally or add new stuff to it?

That is one of the motivations for archiving histories yes.

[hexylena]

@davelopez if we can we easily tell from an e.g. API call (as anonymous external users) whether those histories are archived or not, we can add linting to ensure those histories are archived (it's a good point @bgruening!)

[davelopez]

Sure, every history API call will contain an "archived" flag telling you so: https://usegalaxy.eu/api/histories/0fc6b637aadbc8a2?view=summary

[hexylena]

I was not familiar with the ?view=summary key before, interesting. What other views are available?

[davelopez]

Here is the list of views available to histories: https://github.com/galaxyproject/galaxy/blob/d18bc6855df1d168394778658cd108be67004650/lib/galaxy/managers/histories.py#L776

You can also get a specific set of fields using keys:
https://usegalaxy.eu/api/histories/0fc6b637aadbc8a2?keys=name,archived

[hexylena]

oh, very useful to know, thank you!

[bgruening]

Sorry for derailing this PR.