Where communities thrive


  • Join over 1.5M+ people
  • Join over 100K+ communities
  • Free without limits
  • Create your own community
People
Repo info
Activity
    Simon Bray
    @simonbray:matrix.org
    [m]
    Thanks for having a look Marius!
    I will test it tomorrow on the real workflow, but I'm sure that's it
    Simon Bray
    @simonbray:matrix.org
    [m]
    Could I have a review of galaxyproject/iwc#68, when someone has time, from a technical, IWC point of view?
    Chris Barnett agreed to review it from the scientific side
    Marius
    @mvdbeek:matrix.org
    [m]
    I'm at the biohackathon, but I can take a look early next week
    Simon Bray
    @simonbray:matrix.org
    [m]
    that would be great, thanks Marius
    Marius
    @mvdbeek:matrix.org
    [m]
    If you want to get the tests passing you could take a look into either installing the tools on usegalaxy.org via https://github.com/galaxyproject/usegalaxy-tools or seeing if we can remove --no_shed_install from https://github.com/galaxyproject/planemo-ci-action/blob/main/planemo_ci_actions.sh#L6
    We could probably copy /cvmfs/main.galaxyproject.org/config/shed_tool_conf.xml to a writable location and then planemo would install the tools that are not available on cvmfs ... or that would be my hope
    Simon Bray
    @simonbray:matrix.org
    [m]
    hm, in the latter case you would switch to testing on a local galaxy, not on usegalaxy.org, right?
    Marius
    @mvdbeek:matrix.org
    [m]
    it is all local
    just the tools and reference data come from cvmfs
    Simon Bray
    @simonbray:matrix.org
    [m]
    ah ok, that makes sense
    so you don't have to reinstall the tools each time
    Marius
    @mvdbeek:matrix.org
    [m]
    exactly ... although it also takes a long time to start up, if we load all the tools that we don't actually use, maybe we'd be better off to just have the reference data on cvmfs
    and test against live servers as separate jobs
    Helena Rasche
    @hexylena:matrix.org
    [m]
    Do we have anything for generating RO Crates from workflows? I've had a quick google and found nothing
    but the WorkflowHub people finally seem to have an API so maybe we can do that in the GTN
    wm75 (Wolfgang Maier)
    @wm75:matrix.org
    [m]
    Helena Rasche
    @hexylena:matrix.org
    [m]
    ahh future plans
    that might be just the ticket, thanks wm75 (Wolfgang Maier)
    oh and built in upload to WFH? fab
    ok, yeah that might be it
    Marius
    @mvdbeek:matrix.org
    [m]
    yes, but please push them towards a github app. this is just insane that we have to do this
    Simon Bray
    @simonbray:matrix.org
    [m]
    Hello, no pressure, but just a reminder that this PR is still open: galaxyproject/iwc#68
    we would like to publish a paper referring to these workflows by the end of December, and it would be ideal if they were in the IWC by then
    Marius
    @mvdbeek:matrix.org
    [m]
    I think you're missing the .dockstore.yml file for running the tests
    Nope, but no idea why the tests didn't run
    Simon Bray
    @simonbray:matrix.org
    [m]
    No, they are there - the other issue is galaxyproject/usegalaxy-tools#441
    Marius
    @mvdbeek:matrix.org
    [m]
    This is amazing, I'll make sure we get this deployed ASAP
    Simon Bray
    @simonbray:matrix.org
    [m]
    Thanks a lot! Do you have any comment here: https://github.com/galaxyproject/iwc/pull/68#discussion_r757525658
    Marius
    @mvdbeek:matrix.org
    [m]
    Hmm, I don't think that's too bad ... it's not that different from downloading accessions from the sra for instance. I guess it would be cool if we could have an optional data input with a default that fetches the file
    Marius
    @mvdbeek:matrix.org
    [m]
    The tools are deployed and should be on cvmfs in ~ 30 minutes
    Simon Bray
    @simonbray:matrix.org
    [m]
    nice, thank you

    Hmm, I don't think that's too bad ... it's not that different from downloading accessions from the sra for instance. I guess it would be cool if we could have an optional data input with a default that fetches the file

    yes, I had thought of that, but I'm not sure if there is a easy way to implement it

    I will have a think
    Simon Bray
    @simonbray:matrix.org
    [m]
    Basically it would be the same functionality as the upload tool
    Marius
    @mvdbeek:matrix.org
    [m]
    Yeah, we don't have any obvious way to do it, I think. CWL does have the concept of default file values, I think we'd need to mirror something like that
    Or a little more intricate, you could have a conditional step that only runs if no input dataset has been provided
    Neither of the 2 things are implemented though. On the roadmap, but it might take a while
    https://github.com/common-workflow-lab/galaxy/pull/123/commits/7412df6a9bb00d24b53a0a83815929c04c30c5e4 was halfway there, but got stuck on the way we map over invocations
    Simon Bray
    @simonbray:matrix.org
    [m]
    yes, it would be great if conditionals could be supported at some point
    another question about that PR: is there a recommended way to deal with subworkflows? One of the workflows in that PR is a subworkflow used by two of the others.
    Marius
    @mvdbeek:matrix.org
    [m]
    I would duplicate them for now and mention this in the readme, which I think you've done already. Ultimately it would be cool if we could just reference the subworkflow by URI
    The .ga files still need a "release": "0.1" field
    Cristóbal Gallardo
    @gallardoalba:matrix.org
    [m]
    wm75 (Wolfgang Maier)
    @wm75:matrix.org
    [m]
    No, I don't think there is a bulk import way.
    Not sure whether it's really that important to have one either for workflows. Realistically, when do you ever want to import so many that you cannot do it one by one?
    Cristóbal Gallardo
    @gallardoalba:matrix.org
    [m]
    Thanks! Also Simon proposed my to suggest the user to create a script by using Bioblend.
    Simon Bray
    @simonbray:matrix.org
    [m]
    maybe the user wants to port them between two servers? that's the only usecase I can imagine
    Simon Bray
    @simonbray:matrix.org
    [m]
    I see the new workflows I added to the IWC are now in WFH, but not yet in Dockstore. I'm wondering if this is unexpected or if the deployment generally takes longer?