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Repo info
Activity
    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?
    Marius
    @mvdbeek:matrix.org
    [m]
    We need to add an additional field to .dockstore.yml, else we have to do it manually
    One sec
    Simon Bray
    @simonbray:matrix.org
    [m]
    Thanks! Unfortunately there's a typo in the URL - would it be possible to fix that?
    Chemistory
    Marius
    @mvdbeek:matrix.org
    [m]
    Should be possible, yeah
    Do you have an account on dockstore ? I could add you as admin there
    We can put a few more details on the Computational Chemistry collection page
    Simon Bray
    @simonbray:matrix.org
    [m]
    Yes, simonbray
    Marius
    @mvdbeek:matrix.org
    [m]
    Alright, I think you should have an invitation
    Simon Bray
    @simonbray:matrix.org
    [m]
    Yep, accepted 👍️
    bwlang
    @bwlang:matrix.org
    [m]
    looks like pangolin in iwc workflows is not working - maybe an upstream change? Anybody already working on this?
    bgruening
    @bgruening:matrix.org
    [m]
    What is the error?
    bwlang
    @bwlang:matrix.org
    [m]

    hard to tell... but this is what's in stdout
    you dont' see this error too?
    i see it on my local galaxy and usegalaxy.eu
    pangolearn updated to 2021-11-25
    constellations updated to v0.0.29
    pango-designation updated to v1.2.110
    Job stats:
    job count min threads max threads


    align_to_reference 1 1 1
    all 1 1 1
    get_constellations 1 1 1
    hash_sequence_assign 1 1 1
    scorpio 1 8 8
    use_usher 1 8 8
    usher_to_report 1 1 1
    total 7 1 8

    Warning: couldn't parse the following string: # nuc:G11287T
    [Sun Dec 12 13:25:05 2021]
    Error in rule get_constellations:
    jobid: 6
    output: /data/jwd/main/036/355/36355745/tmp/tmpknha9g5m/get_constellations.txt
    shell:

        scorpio list         --constellations /data/jwd/main/036/355/36355745/working/datadir/constellations/definitions/cA.23.1+E484K.json /data/jwd/main/036/355/36355745/working/datadir/constellations/definitions/cA.23.1.json /data/jwd/main/036/355/36355745/working/datadir/constellations/definitions/cAV1.json /data/jwd/main/036/355/36355745/working/datadir/constellations/definitions/cAY.4.2.json /data/jwd/main/036/355/36355745/working/datadir/constellations/definitions/cAY.4.json /data/jwd/main/036/355/36355745/working/datadir/constellations/definitions/cB.1.1.318.json /data/jwd/main/036/355/36355745/working/datadir/constellations/definitions/cB.1.1.529.json /data/jwd/main/036/355/36355745/working/datadir/constellations/definitions/cB.1.1.7+E484K.json /data/jwd/main/036/355/36355745/working/datadir/constellations/definitions/cB.1.1.7.json /data/jwd/main/036/355/36355745/working/datadir/constellations/definitions/cB.1.351.json /data/jwd/main/036/355/36355745/working/datadir/constellations/definitions/cB.1.427.json /data/jwd/main/036/355/36355745/working/datadir/constellations/definitions/cB.1.429.json /data/jwd/main/036/355/36355745/working/datadir/constellations/definitions/cB.1.525.json /data/jwd/main/036/355/36355745/working/datadir/constellations/definitions/cB.1.526.json /data/jwd/main/036/355/36355745/working/datadir/constellations/definitions/cB.1.617.1.json /data/jwd/main/036/355/36355745/working/datadir/constellations/definitions/cB.1.617.2+K417N.json /data/jwd/main/036/355/36355745/working/datadir/constellations/definitions/cB.1.617.2.json /data/jwd/main/036/355/36355745/working/datadir/constellations/definitions/cB.1.617.3.json /data/jwd/main/036/355/36355745/working/datadir/constellations/definitions/cB.1.621.json /data/jwd/main/036/355/36355745/working/datadir/constellations/definitions/cBA.1.json /data/jwd/main/036/355/36355745/working/datadir/constellations/definitions/cBA.1_probable.json /data/jwd/main/036/355/36355745/working/datadir/constellations/definitions/cBA.2.json /data/jwd/main/036/355/36355745/working/datadir/constellations/definitions/cC.37.json /data/jwd/main/036/355/36355745/working/datadir/constellations/definitions/cP.1.json /data/jwd/main/036/355/36355745/working/datadir/constellations/definitions/cP.2.json /data/jwd/main/036/355/36355745/working/datadir/constellations/definitions/cP.3.json         --pangolin > /data/jwd/main/036/355/36355745/tmp/tmpknha9g5m/get_constellations.txt
    
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

    Exiting because a job execution failed. Look above for error message

    here's a history that ran earlier and is now failing (https://usegalaxy.eu/u/brad_langhorst/h/1115-positive-run2-dada)
    444 worked, 446 fails
    wm75 (Wolfgang Maier)
    @wm75:matrix.org
    [m]
    Had a failing rerun of pangolin early on Friday, too, but didn't check what happened and simply hoped it was some temporary issue. Looks like it's not :(
    Marius
    @mvdbeek:matrix.org
    [m]
    Is it worth to re-run the tests on github ?
    Triggered a re-run for everything in galaxyproject/iwc#73 ... we'll need to tune the command a bit so we can run a specific workflow
    bgruening
    @bgruening:matrix.org
    [m]
    It seems that it is the latest pangoLEARN version
    if you use an older version (not from weg) but the local install version from 2021-10-18 it works
    bgruening
    @bgruening:matrix.org
    [m]
    The last working version seems to be 2021-11-25
    I have installed this one
    and you can now run your pangolin with this version instead of latest version from web
    but this version does not seem to have Omicron included yet
    :(
    wm75 (Wolfgang Maier)
    @wm75:matrix.org
    [m]
    Uh, really weird cause I got B.1.1.529 annotated with latest from web until Wednesday last week.