Optimizing Galaxy for Teaching: what could be improved? #2198
Replies: 12 comments 24 replies
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When users look at their multi-history view, they often ask if they can see the creation date of the history. I have been telling them to name their histories with the date, but perhaps the overview can show creation date and possibly a "last updated on" date at the top?
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Yes! This should be a super easy paper cut. It looks like there's already an open issue from @fubar2 galaxyproject/galaxy#10455 |
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Maybe THE major point I often heard from users / trainees, is related to the fact their is too much tools and this is hard to find the right tool... I konw that this is an old issue, and there was a lot of improvements, but it is still a real concern... Additionnaly to that, the search functionality is often not very usefull as let too much unrelated tools on the filtered list and/or the one searched is not there for obvious reason... Is there any manner to propose a maybe more complex / detailled mutlicriteria tool serach form ? Or others ? Thanks Saskia to create this discussion, and sorry if it is not supposed to be used directly as I do ;) |
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@yvanlebras yes, this is EXACTLY what this discussion is for, thanks! We will communicate these obseservations from trainers to the Galaxy UI/UX team regularly so that they are aware of some of the pain points experienced by users. I agree, especially for new users, the tool form feels very overwhelming, it would be great if they could have more control over this. Starring/Favoriting tools is definitely a step in the right directlon, but perhaps this can be expanded to support a custom user-defined view of the tool panel, where users can add tools from the full list of available tools orso, create their own section names, etc, to build up their own tool panel? |
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Maybe it would be possible to build smaller tool panels based on the tool list of each tutorial? |
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We've definitely discussed that @abretaud on the GTN side, it would be super cool. What's missing is that Galaxy knows which tutorial you're doing. It gets closer with the GTN-in-Galaxy, but, the connection is still missing and I'm not sure of a good way to integrate that :( With the GTN in Galaxy webhook we could show a list of the tools on the left like a mini tool panel/ but still not super nice.... |
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Watching some of the videos for Smorgasbord, I noticed a lot of instructors spend quite some time renaming datasets after import from URL. It would be nice if the upload form included an option to strip the full URL, and keeping only the filename. (and perhaps capturing the full URL as an annotation orso to save the info about its origin) |
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I'd like the option to rename a dataset before hitting RUN on a tool. That actually drags a surprisingly annoying amount of time in running a tutorial, because the tool finally finishes and then BAM you have to run a data change again. Also, I found a glitch with Manipulate AnnData wherein it runs fine but you can't rename it, so might avoid those issues in the future. All in all, might help keep people more organised and makes generating labels part of the tool rather than an overly zealous addition |
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Getting different colour options in workflows would help for showing different sections and overall using the nice workflow editor in teaching |
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Jupyter in Galaxy - it is always a bit weird with interactive environments as they look perpetually on in the history, even if you close them. Trying to share a notebook, for example, will fail the second you stop your own environment, so sharability isn't great unless you leave it open infinitely. |
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@nomadscientist the intention is that you export your notebook to your history. And share the notebook file, the ipynb file. |
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Ahhh ok. Fair enough. I think it's easy to get lax with Galaxy being so good at saving everything, that having to remember to save frequently AND export in the Jupyter environment can get you, but that does work and makes sense. |
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@bgruening I can confirm that this does not work within Galaxy. So if you push your notebook to your galaxy history, close the visualisation and/or share your history with someone else, they cannot open that notebook in Galaxy JupyterLab (either by calling it as a notebook or by calling it a dataset). Either way it glitches out. The only way to do it (as far as I can tell) is to download the notebook onto your computer, then upload it within the JupyterLab. |
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Retroactively adding tags would be amazing - "Oh no, my history is a mess, I have two different paths running and I keep confusing them, how will I fix this?" --> goes to step 2, where I added a normalisation parameter differently for one set of analysis to compare with another, and adds a tag, and magically all of the following datasets that originated from that one suddenly have a tag. Glorious. |
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You can try to use the script: https://github.com/galaxyproject/galaxy/blob/dev/scripts/apply_tags.py to retroactively add tags to datasets in Galaxy history. |
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Is that a tool? Is there a tool 'apply tags'? That would be amazing |
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It's not a tool, it's a script within the galaxy codebase. So it's a bit less easy to run for non-techie users, we should really fix this in the UI side of galaxy :( The tool "apply tags" in galaxy does something confusingly different! hah |
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'Hands-On' that can collapse down (like question/answers, but auto-set to be expanded). Just, you tend to scroll a lot with tutorials, so that might be handy |
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Like 'yes, did that, tick' <--- or even a tick box omg |
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Oh I like the tick box idea! It's really nice. |
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It would be nice if ORCID somehow picked up the GTN tutorials/slide decks etc. Currently it doesn't, so I need to make a Bibtext thing and import it and it's a whole debacle. |
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There's the automatic bibtex thing at the bottom, or does that not help?
Automatically submitting data to ORCID's API however requires a "member" api key, and their membership is not cheap :( https://info.orcid.org/about-membership/ so looks like that's a no-go |
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That is RUBBISH. Bad orchid |
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Filed as galaxyproject/galaxy#13258 |
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The EYE button should look DIFFERENT depending on whether it starts DOWNLOADING a dataset vs SHOWS you the dataset |
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It really really should only ever show the dataset, is there a specific datatype that is resulting in a download? |
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AnnData - https://usegalaxy.eu/u/wendi.bacon/h/imported-spanscriptomics-continuacin |
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Ahh it's an |
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Oh also rdata - see 5:55s here: https://www.youtube.com/watch?v=nfAUXP3W-jM |
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Workflow ranking! |
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Incidentally could help with other stuff, example - could embed website view of searching workflows for 'single-cell' on the single-cell training page |
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As instructors, we have a unique perspective by frequently watching people use Galaxy for analysis and/or for the first time. Did you observe them struggling with specific tasks? Have ideas for how to streamline how people interact with Galaxy? Missing features? Any other ideas for how Galaxy can be improved for end-users? Please let us know here!
We will communicate these training priorities to the Galaxy Development team, see this project board
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