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    Nolan Woods
    @innovate-invent
    is there now a default input sanitizer applied to all inputs? it is breaking tools
    @bgruening:matrix.org your cut tool is broken, it is adding __cn__ between each field number
    I am also seeing this escaping in other tools where it shouldn't be applied
    Nolan Woods
    @innovate-invent
    cut only seems to have an issue in a workflow
    Nolan Woods
    @innovate-invent
    another nasty bug: galaxyproject/galaxy#14589
    Nolan Woods
    @innovate-invent
    if anyone feels like looking into another annoying bug: galaxyproject/galaxy#14601
    wm75 (Wolfgang Maier)
    @wm75:matrix.org
    [m]
    @innovate-invent: There seems to be an issue in how the selection for:
    <param name="list" type="data_column" data_ref="input" multiple="true" label="List of Fields" help="(-f)"/>
    gets extracted into a workflow step. The columns should not have become separated by newlines in the first place in that workflow file of yours (but I can confirm that this is what happens currently when you extract a workflow from a history containing such a step.
    The newlines then get sanititzed to __cn__, which is regular behavior.
    What you can do to get things working for now is edit the .ga file manually to replace the newline characters with ,.
    If you import that fixed workflow file and run it directly, things should work. However, every time you open the WF in the WF editor, it will convert the commas to newlines again :(
    Nolan Woods
    @innovate-invent
    Interesting, thanks @wm75:matrix.org . I hadn't realised the newlines were in the workflow itself.
    David Managadze
    @helixomics_twitter
    Hi, what is a proper way to run a sudo command inside a Galaxy tool? I'd like to archive /export folder (simpler than dealing with Docker volumes) and it does not let me do it because user galaxy does not have permission to the /export/postgresql/ folder.
    bgruening
    @bgruening:matrix.org
    [m]
    I'm not sure that is the best way to do it. What problems did you have with archiving the volumes?
    David Managadze
    @helixomics_twitter
    Oh, hi Björn, did not expect you to be online and respond! First of all, thank you for all your work and time spent for this!
    I am trying to build a tool that will save the full state, "take a snapshot", of the Galaxy, with its history files, workflows, etc, and save it externally to cloud. To do so, I thing I should built a tool that a user can call, and the tool will archive the /export with all its content. Next time, I start Galaxy with that state (i.e. unarchive it first and attach as a volume). Do you think this is not a good approach? What would be better?
    @bgruening:matrix.org , you'd suggest to use a docker volume? Then how can I access the volume "from outside" to archive it? I thought to attach docker.sock and run the Galaxy image in --privileged mode but since this approach is generally discouraged, I thought to simply archive the /export/.
    bgruening
    @bgruening:matrix.org
    [m]
    Do you want the user to archive the state or the admin, who runs the Docker container?
    Is that a single user instance?
    David Managadze
    @helixomics_twitter
    user needs to be able to do this.
    This is actually a single user case. (I'd also definitely prefer to use sqlite instead of postgres, as well as run the minimalistic setup but I am getting some errors from startup_liteso I postponed troubleshooting that.)
    bgruening
    @bgruening:matrix.org
    [m]
    Mh, how do you envision to restore the state?
    Should also the user be able to do that?
    David Managadze
    @helixomics_twitter
    yes
    :)
    bgruening
    @bgruening:matrix.org
    [m]
    But a tool would not work here. You can not run a tool that replaces itself.
    So I guess we need to find a different model to archive that
    David Managadze
    @helixomics_twitter
    @bgruening:matrix.org , I am building Galaxy on a cloud platform where it will run like an app. During start, user will say "I want to run the Galaxy app and use this snapshot/state file". The app will do some preprocessing: unarchive the snapshot/state file to a folder and then docker run ... -v snapshot:/export galaxy.
    So, if I somehow manage to archive the /export folder from within the tool (and then upload to cloud) it should work.
    bgruening
    @bgruening:matrix.org
    [m]
    But why not do it outside the container. If the user already chooses which snapshot to start with... On the same side you could say 3 galaxy's running... Do you want to stop one and archive?
    Btw this pretty much sounds like the cloudman usecase
    Have a look at cloudman :-)
    David Managadze
    @helixomics_twitter
    RE Do you want to stop one and archive? - where, from what interface do you "say" this?
    RE cloudman usecase - I did not know about this, am reading now, may not be what we need...
    Nolan Woods
    @innovate-invent
    is anyone aware of a recent commit to 22.05 that would have reverted galaxyproject/galaxy#14473
    Nolan Woods
    @innovate-invent
    Looks like the workflow has to be reloaded every time you insert a subworkflow..
    Nolan Woods
    @innovate-invent
    Is there any way to make a subworkflow output not a output of its parent?
    1 reply
    Marius
    @mvdbeek:matrix.org
    [m]
    It would be more useful if you could say what isn't working. That PR comes with 2 tests that verify the desired behavior
    David Managadze
    @helixomics_twitter
    Is it possible to shutdown the Galaxy web app and everything with it from the UI?
    I am building a single-user instance and I want user to have "a button" (or a tool) on the screen that they can click to shut the whole thing down. (Also save the state, but that's a different story.)
    martenson
    @martenson:matrix.org
    [m]
    @helixomics_twitter: you can stop accepting jobs from the UI as an admin, but you cannot turn the instance off using the UI afaik
    David Managadze
    @helixomics_twitter
    @martenson:matrix.org , yeah... I'd like to build a one-click solution to do all that...
    martenson
    @martenson:matrix.org
    [m]
    Galaxy process is usually run by a manager that has little to do with Galaxy UI so that is not going to be straight forward I am afraid.
    David Managadze
    @helixomics_twitter
    If this does not work, I am thinking to create a tool that a user can run. The tool will create a sentinel/flag file. An outside script that started the container will look for the appearance of this sentinel file; if exists, shutdown the galaxy and continue the process.
    Nolan Woods
    @innovate-invent
    @mvdbeek:matrix.org sorry, the change datatype PJA does not take effect until the page is reloaded with the workflow inserted
    I thought that it was completely reverted, but I must have already had the subworkflow inserted when I initially tested it
    M Bernt
    @bernt-matthias:matrix.org
    [m]
    May I ask for reviews on two tool linting PR
    elichad
    @elichad:matrix.org
    [m]
    Anyone else having trouble joining the community call? The link isn't working for me (502 Bad Gateway)
    Alex Ostrovsky
    @astrovsky01:matrix.org
    [m]
    Assunta DeSanto
    @assuntad23:matrix.org
    [m]
    Can someone re-run this for me? galaxyproject/galaxy#14646
    M Bernt
    @bernt-matthias:matrix.org
    [m]
    1 reply
    Nolan Woods
    @innovate-invent
    does anyone else get an error when they impersonate a user in 22.05?
    dannon
    @dannon:matrix.org
    [m]
    @innovate-invent: I haven't noticed any issues, it's still working fine for me.
    Jennifer Hillman-Jackson
    @jennaj:matrix.org
    [m]
    Same
    Helena
    @hexylena:matrix.org
    [m]

    hey y'all, I'm writing a quick python typing tutorial for one of my jobs, the target audience is "intermediate python programmers"

    If anyone has comments or opinions on this topic, I'd love your input on the draft tutorial I've written which covers some of the main motivation but maybe other folks would know if it's misisng anything important?

    https://github.com/galaxyproject/training-material/pull/3634/commits/bed632a7c2d92b8eb827d7bdd92236855d2d5f54