feat: make resources file downloadable via select workflow page

[Smeds]

Description

This pull-request will make resources generated by Hiram and Nate more accessible for user by providing links to them.

Fill free to make changes to formatting and title names, if you have any good suggestions.

Related Issue

This pull-request address the following issues:

• [GA2] Make resources file downloadable via Select Workflow page #932
• [GA2] Make assembly indices available #933

[Smeds]

@NoopDog It would be great if we could have this looked at during this week. We said that for Genomic Informatics we would have the site in beta stage, and it would be nice to have some changes added between alpha and beta.

[d-callan]

thanks for this, its kind of a cool idea.

some high level thoughts/ questions:

1. is this a thing diverging from brc? or something we should try to make sure is implemented generally so both can use?
2. who are we trying to support w this? is there overlap in use case w the no/ custom workflow thing? or is this for ppl not in galaxy?
3. can we consider alternative ux? not sure i like just listing things out like that in the right panel. either make each of the sub heading collapsible, or put the actual links all collected together on another page and just link to them, idk. its just visually a lot of clutter for something i suspect isnt a primary use case.

[Smeds]

1. is this a thing diverging from brc? or something we should try to make sure is implemented generally so both can use?
   We should be able implement this for both ga2 and brc. For brc we could display the stuff Nate are creating, and it would be really easy only requiring the assmebly.json file to have a field named assemblyResources storing a dict where the keys are used as title.

"assemblyResources": {
      "Assembly": [
        {
          "name": "GCA_003287225.2.2bit",
          "url": "https://js2.jetstream-cloud.org:8001/genomeark/alignment/primary/mammals/GCA_003287225.2.2bit"
        },
        {
          "name": "GCA_003287225.2.fa.gz",
          "url": "https://js2.jetstream-cloud.org:8001/genomeark/alignment/primary/mammals/GCA_003287225.2.fa.gz"
        }
      ],
      "Repeat": [
        {
          "name": "GCA_003287225.2.repeatModeler.families.fa.gz",
          "url": "https://js2.jetstream-cloud.org:8001/genomeark/alignment/primary/mammals/GCA_003287225.2.repeatModeler.families.fa.gz"
        }
      ]
    },

2. who are we trying to support w this? is there overlap in use case w the no/ custom workflow thing? or is this for ppl not in galaxy?

This would be most useful for people who aren’t using Galaxy, or at least not using the instances we host. As I recall, with VGP and GA2 we’ve said that we should aim to support other platforms as well, if not right away, then in the future. @nekrut

I think one thing we want to provide is a place where it's easy for researchers to locate links to different resources.

3. can we consider alternative ux? not sure i like just listing things out like that in the right panel. either make each of the sub heading collapsible, or put the actual links all collected together on another page and just link to them, idk. its just visually a lot of clutter for something i suspect isnt a primary use case.

I’m open to UX changes, this is just a first version. One possible solution, as you mentioned, could be to use a separate page. We have data that could be interesting for new analyses; the links in this pull request are examples of that. However, GA2 will also include resources useful to researchers that aren’t directly tied to new analyses, for example, QC reports and pretext data that can be valuable when evaluating an assembly or the data used to build it.

@d-callan

[d-callan]

Thanks, I'm personally inclined to a new page and a single new link under resources on the existing page. Since I think this makes sense for BRC also, let's try to talk about it on a Mon call.

[Smeds]

Thanks, I'm personally inclined to a new page and a single new link under resources on the existing page. Since I think this makes sense for BRC also, let's try to talk about it on a Mon call.

This could be a simple solution! If we decide to create a new page for the resource, we could also add a link to it from the “View” dropdown on the assembly page.

[NoopDog]

Looks to me like what you want here is a dedicated page for the assembly, with a list of all related resources hanging off it that you can download as a TSV or individually. Looks like there is:

1. The assembly itself
2. UCSC tracks for the assembly
3. The index files in Galaxy.

I can get a mock in the next few days to explain myself better.

[Smeds]

Looks to me like what you want here is a dedicated page for the assembly, with a list of all related resources hanging off it that you can download as a TSV or individually. Looks like there is:

1. The assembly itself

2. UCSC tracks for the assembly

3. The index files in Galaxy.

I can get a mock in the next few days to explain myself better.

soon we will probably also have jbrowse files for the assemblies

[NoopDog]

Ok thx I can get a mock up created.

[Smeds]

@NoopDog Have you had time to look into creating a mock up?

[Smeds]

@NoopDog Have you had time to look into creating a mock up?