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Repo info
Activity
    Marius
    @mvdbeek:matrix.org
    [m]
    I bet the problem is the step order and the workflow run form submitting the input by the step order. This is all such a bad idea :/
    And impossible to debug too, because once you open the workflow in the editor you get a new step order
    Which shouldn't be persisted at all .... but that's just me, unreasonably expecting reasonable things 🤷
    Marius
    @mvdbeek:matrix.org
    [m]
    :point_up: Edit: I bet the problem is the step order and the workflow run form submitting the input by the step order. This is all such a bad idea :/. We've known that doesn't work and have a better submission API for 10 years now
    John Chilton
    @jmchilton:matrix.org
    [m]
    The newer workflow form uses the better API right? Or are you saying the older API was better?
    Marius
    @mvdbeek:matrix.org
    [m]
    We're using the new API endpoint, but submissionis currently using inputs_by: "step_index"
    Could be a regression
    That's just asking for trouble IMO
    M Bernt
    @bernt-matthias:matrix.org
    [m]
    Has anyone experience with porting knime workflows / tools to Galaxy?
    bgruening
    @bgruening:matrix.org
    [m]
    We have done this manually, automatic was and probably is not possible
    M Bernt
    @bernt-matthias:matrix.org
    [m]
    Is there somewhere docs how tools/workflows are defined in the Knime world?
    An automatic conversion would also be of interest for the OpenMS community .. they started to develop workflows for both worlds (Galaxy part is still ongoing)
    bgruening
    @bgruening:matrix.org
    [m]
    no idea
    the OpenMS people are the best to ask
    they have invested a lot in this system
    Cristóbal Gallardo
    @gallardoalba:matrix.org
    [m]
    Hi all! I'm getting this error when running planemo test hifiasm-assembly.ga --galaxy_url http://127.0.0.1:8080 --galaxy_user_key 60ae07c799836b135125c4972e2d42c8:
    File "/home/laptop/.local/lib/python3.8/site-packages/galaxy/tool_util/cwl/util.py", line 441, in dataset_dict_to_json_content return json.safe_load(f) AttributeError: module 'json' has no attribute 'safe_load' Any hint about how to solve it?
    Nicola Soranzo
    @nsoranzo:matrix.org
    [m]
    Is this using some CWL tool?
    The error has been fixed upstream but not yet released in a new galaxy-tool-util package.
    Cristóbal Gallardo
    @gallardoalba:matrix.org
    [m]
    Ah cool. This error is also reported in GitHub; I just realised about it.
    Nicola Soranzo
    @nsoranzo:matrix.org
    [m]
    Pre-print that could be of interest: https://doi.org/10.1101/2022.07.08.499265
    pvanheusden
    @pvanheusden:matrix.org
    [m]
    this was presented at BOSC, right? I saw these people present on a recent CWL call
    1 reply
    Marius
    @mvdbeek:matrix.org
    [m]

    We've got a meeting scheduled in 15 minutes, I'll be around if anyone wants to chat.

    Workflow WG monthly call
    Monday, 15 August · 16:00 – 17:00
    Google Meet joining info
    Video call link: https://meet.google.com/myu-vozy-bsj

    Delphine Lariviere
    @delphine-l:matrix.org
    [m]

    Hi, the tests are failing for one of my workflows with this error message

    There were problems with 1 test(s) - out of 1 test(s) executed. See /home/runner/work/iwc/iwc/tool_test_output.html for detailed breakdown.
    Traceback (most recent call last):
      File "/opt/hostedtoolcache/Python/3.7.13/x64/lib/python3.7/site-packages/planemo/galaxy/activity.py", line 53, in execute
        return _execute(ctx, config, runnable, job_path, **kwds)
      File "/opt/hostedtoolcache/Python/3.7.13/x64/lib/python3.7/site-packages/planemo/galaxy/activity.py", line 174, in _execute
        inputs_by="name",
      File "/opt/hostedtoolcache/Python/3.7.13/x64/lib/python3.7/site-packages/bioblend/galaxy/workflows/__init__.py", line 485, in invoke_workflow
        return self._post(payload, url=url)
      File "/opt/hostedtoolcache/Python/3.7.13/x64/lib/python3.7/site-packages/bioblend/galaxy/client.py", line 190, in _post
        return self.gi.make_post_request(url, payload=payload, files_attached=files_attached)
      File "/opt/hostedtoolcache/Python/3.7.13/x64/lib/python3.7/site-packages/bioblend/galaxyclient.py", line 159, in make_post_request
        status_code=r.status_code,
    bioblend.ConnectionError: Unexpected HTTP status code: 400: {"err_msg": "Workflow was not invoked; the following required tools are not installed: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_dustmasker_wrapper/2.10.1+galaxy1 (version 2.10.1+galaxy1), toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.10.1+galaxy2 (version 2.10.1+galaxy2), toolshed.g2.bx.psu.edu/repos/iuc/parse_mito_blast/parse_mito_blast/1.0.2+galaxy0 (version 1.0.2+galaxy0)", "err_code": 0, "traceback": "Traceback (most recent call last):\n  File \"/tmp/tmpmaykmxbh/galaxy-dev/lib/galaxy/web/framework/decorators.py\", line 320, in decorator\n    rval = func(self, trans, *args, **kwargs)\n  File \"/tmp/tmpmaykmxbh/galaxy-dev/lib/galaxy/webapps/galaxy/api/workflows.py\", line 776, in invoke\n    raise exceptions.MessageException(missing_tools_message)\ngalaxy.exceptions.MessageException: Workflow was not invoked; the following required tools are not installed: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_dustmasker_wrapper/2.10.1+galaxy1 (version 2.10.1+galaxy1), toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.10.1+galaxy2 (version 2.10.1+galaxy2), toolshed.g2.bx.psu.edu/repos/iuc/parse_mito_blast/parse_mito_blast/1.0.2+galaxy0 (version 1.0.2+galaxy0)\n"}
    Galaxy-Workflow-VGP_assembly_decontamination_pipeline.ga_0: failed

    I am not sure where to look to fix that,

    Marius
    @mvdbeek:matrix.org
    [m]
    Those tools aren't installed in main, that's easy to fix
    Delphine Lariviere
    @delphine-l:matrix.org
    [m]
    the github actions are run on main ? I'll install the tools then
    thanks
    Marius
    @mvdbeek:matrix.org
    [m]
    No, but they can only run with the tools that are installed on main
    Delphine Lariviere
    @delphine-l:matrix.org
    [m]
    I installed the tool but it still doesn't seem to be running the tests, could someone take a look at it, I don't understand the error : https://github.com/Delphine-L/iwc/actions/runs/2870582438
    Nicola Soranzo
    @nsoranzo:matrix.org
    [m]
    Marius
    @mvdbeek:matrix.org
    [m]
    Hope y'all can join the call in 40 minutes!
    Workflow WG monthly call
    Monday, 19 September · 16:00 – 17:00
    Google Meet joining info
    Video call link: https://meet.google.com/myu-vozy-bsj
    wm75 (Wolfgang Maier)
    @wm75:matrix.org
    [m]
    I'm in a session at ECCB still until 16:30 :(
    davelopez (David López)
    @davel0pez:matrix.org
    [m]
    I'll hop in, to listen 🙂
    John Chilton
    @jmchilton:matrix.org
    [m]
    I think I've put together objectives and an unfortunately high-level technical plan for the tool state rewrite project (https://docs.google.com/document/d/1HQOLpLN54CjrB-wbD463XqzvUm-dNB8vTXUFBExh_2o/edit). It is at the top of the GCC notes
    bwlang
    @bwlang:matrix.org
    [m]
    I'd like to cite the iWC and https://github.com/iwc-workflows/sars-cov-2-pe-illumina-artic-variant-calling specifically in a paper I'm working on. I did not quickly find something in pubmed... is there a preferred thing to cite (maybe with a DOI?)
    wm75 (Wolfgang Maier)
    @wm75:matrix.org
    [m]
    bwlang: This is what I wrote in a manuscript draft:
    Variant calling was then performed with platform-specific Galaxy workflows, which have previously been described [1] and are publically available from Dockstore [2] and the WorkflowHub [3] (https://dockstore.org/organizations/iwc/collections/Covid and https://workflowhub.eu/collections/2, respectively) against NCBI Reference Sequence NC_045512.2.
    
    1. Maier, W., Bray, S., van den Beek, M. et al. Ready-to-use public infrastructure for global SARS-CoV-2 monitoring. Nat Biotechnol. 2021 Sep; 39(10), 11781179. doi: 10.1038/s41587-021-01069-1
    Michael R. Crusoe
    @mr-c:matrix.org
    [m]
    If the maintainer clicks a button , then https://workflowhub.eu/workflows/110?version=7 can get a DOI
    bwlang
    @bwlang:matrix.org
    [m]
    wm75 (Wolfgang Maier) should I wait for you to make a DOI or proceed as you suggested above?
    wm75 (Wolfgang Maier)
    @wm75:matrix.org
    [m]
    I don't think I can create the DOI since the WF on workflowhub was bot-submitted.
    Marius
    @mvdbeek:matrix.org
    [m]
    Does anyone have the bot credentials ?
    I think this might all be in workflowhub hands, I'll see if someone can help us in their slack
    It's not even an IWC specific bot, so I guess they won't hand over credentials
    Michael R. Crusoe
    @mr-c:matrix.org
    [m]
    The SEEK platform has a proper ACL model, so someone ( bgruening ?) should be able to enable a person or an entire team to manage the metadata of these workflows
    Marius
    @mvdbeek:matrix.org
    [m]
    Yep, I got a response, I'll get those permissions, but also automatic DOIs are an option
    Marius
    @mvdbeek:matrix.org
    [m]
    Maier, W. (2022). sars-cov-2-pe-illumina-artic-variant-calling/COVID-19-PE-ARTIC-ILLUMINA. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.110.7
    bwlang
    @bwlang:matrix.org
    [m]
    awesome - I guess we should put together an IWC paper some time soon too so that can be easily cited in addition to galaxy itself.
    Marius
    @mvdbeek:matrix.org
    [m]
    Agreed, this is a great idea!