added wkflw run snippets to VGP wkflw tutorial#5132
added wkflw run snippets to VGP wkflw tutorial#5132hexylena merged 15 commits intogalaxyproject:mainfrom
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THE LISTS I WAS SUPPOSED TO FIX ok i can fix that this weekend! edit: i changed the problematic lists to just headers, which i think makes more sense since they're kind of dividing subsections anyway 🤔 |
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| Once we have imported the datasets and the workflows, we can start with the genome assembly. | ||
| All analyses described in this tutorial are performed using *workflows*--chains of tools--shown in [Fig. 1](#figure-1). Specifically, we will use four workflows corresponding to analysis trajectory **B**: 1, 4, 6, and 8. To use these four workflows you need to import them into your Galaxy account following the steps below. Note: these are not necessarily the latest versions of the actual workflows, but versions that have been tested for this tutorial. To see the latest versions, see the [Galaxy Project VGP workflows page](https://galaxyproject.org/projects/vgp/workflows/) and click on the Dockstore links to import workflows. **Alternatively, for each section of the tutorial, there will be a "Launch [workflow] (View on Dockstore)" link at the beginning, which you can use to launch the workflow.** |
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these are not necessarily the latest versions of the actual workflows
But they are the latest versions: you've linked to IDs like github.com/iwc-workflows/kmer-profiling-hifi-VGP1/main which seem to point to the latest version of each workflow. Did you mean to pin these to specific versions instead?
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ACK thank you for catching that!! 🙏🏼 I'll edit the snippets to pin to specific versions, because that would make more sense to prevent people from using latest versions that might not match up with what's presented in this tutorial
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ah, I'm sorry, do you happen to know if there is a way to pin the TRS ID to a specific version? clicking to a different version on the Dockstore page changes just the Source code but not the TRS...
I tried changing it to github.com/iwc-workflows/kmer-profiling-hifi-VGP1/versions/v0.1.5 and github.com/iwc-workflows/kmer-profiling-hifi-VGP1/v0.1.5 but those lead to a 404 error :(
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Huh. When i select an old version on dockstores own launch page, and try and launch it in EU it generated an unversioned url:
that's completely broken useless lol, you select the version once in dockstore and are again presented with a version selector in galaxy? wild.
i'll poke their API in a bit to see what format is required (if it is possible) to generate more specific urls
looks like it was a known issue a while back. so dockstores website is still broken but at least it is possible: galaxyproject/galaxy#12017
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Ok I've added a version parameter (e.g. version="v0.1.5") to the snippet. Could you please add the versions to each snippet usage? :)
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success! adding that parameter makes the URL fill like this: https://usegalaxy.org/workflows/trs_import?trs_server=dockstore.org&run_form=true&trs_id=%23workflow/github.com/iwc-workflows/kmer-profiling-hifi-VGP1/main&trs_version=v0.1.5 and the page that loads automatically loads the wkflw -> wkflw run page. i'll update the snippets to use the version parameter, thank you so much for your help!!
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for the sake of documentation, here's what happens when the snippet specifies a version # that doesn't exist: the user's taken to this page with the "version xyz doesn't exist" message and then they can pick the version 👍🏼
the tutorial's snippets should now all have a version pinned 📌 🚀
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yay!! thank you 🚀 |
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hello! 👋🏼 this edit adds the dockstore workflow launch snippets to the VGP workflow-focused tutorial, and accordingly removes text about importing workflows from github