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Repo info
Activity
    Marius
    @mvdbeek:matrix.org
    [m]
    ok, the test toolshed is up and running on 22.05, but I'll wait for nate before deploying the main tool shed
    Lucille Delisle
    @lldelisle
    Did you try the search for bamleftalign?
    (on the testtoolshed)
    Marius
    @mvdbeek:matrix.org
    [m]
    no
    just bamleftalign blew up of course ๐Ÿ˜†
    Nov 04 13:22:12 eddie.galaxyproject.org gunicorn[68267]: galaxy.web.framework.decorators ERROR 2022-11-04 13:22:12,200 [pN:main,p:68269,tN:WSGI_0] Uncaught exception in exposed API method:
    Nov 04 13:22:12 eddie.galaxyproject.org gunicorn[68267]: Traceback (most recent call last):
    Nov 04 13:22:12 eddie.galaxyproject.org gunicorn[68267]:   File "/srv/toolshed/test/server/lib/galaxy/web/framework/decorators.py", line 337, in decorator
    Nov 04 13:22:12 eddie.galaxyproject.org gunicorn[68267]:     rval = func(self, trans, *args, **kwargs)
    Nov 04 13:22:12 eddie.galaxyproject.org gunicorn[68267]:   File "/srv/toolshed/test/server/lib/tool_shed/webapp/api/repositories.py", line 366, in index
    Nov 04 13:22:12 eddie.galaxyproject.org gunicorn[68267]:     shed, _, owner, name, tool, version = tool_id.split("/")
    Nov 04 13:22:12 eddie.galaxyproject.org gunicorn[68267]: ValueError: not enough values to unpack (expected 6, got 1)
    the api is so ... special
    Marius
    @mvdbeek:matrix.org
    [m]
    returns empty, which might be correct ?
    Sorry the owner is dave
    Lucille Delisle
    @lldelisle
    Youhou
    Marius
    @mvdbeek:matrix.org
    [m]
    this seems about right
    great
    Good job!
    Marius
    @mvdbeek:matrix.org
    [m]
    I'm adding another worker, so the testoolshed will be down for a couple of minutes
    Marius
    @mvdbeek:matrix.org
    [m]
    alright, it's back. if someone wants to try repo creation and update that would be nice
    Lucille Delisle
    @lldelisle
    If my CI works, I should be able to try an update.
    Marius
    @mvdbeek:matrix.org
    [m]
    I didn't hear Nate Coraor say no, so I'll update the main tool shed next
    Nate Coraor
    @natefoo:matrix.org
    [m]
    it's friday you maniac!!@
    Marius
    @mvdbeek:matrix.org
    [m]
    ๐Ÿ˜† it's the tool shed, how much more can I possibly break it ?
    Lucille Delisle
    @lldelisle
    ;-)
    Nate Coraor
    @natefoo:matrix.org
    [m]
    a lot!
    Marius
    @mvdbeek:matrix.org
    [m]
    haha, ok, this isn't urgent, but I won't get around to doing it next week
    dannon
    @dannon:matrix.org
    [m]
    Hold onto that thought! I'm working on ripping all the client code out of the main build and expect to break it again soon.
    (the toolshed)
    wm75 (Wolfgang Maier)
    @wm75:matrix.org
    [m]
    I am currently facing the following issue: I have a tool (https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/vapor/vapor/1.0.2+galaxy2) that expects a multi-sequence FASTA file and, in my case, a list of PE data (representing different samples. The tool will then find the fasta sequence that best matches the reads in each input and will produce a results collection equal in number of elements to the number of PE input samples.
    So far, so good.
    Now, however, I would like to extend this to a collection of multisequence fastas, and I want a run of each sample against each such fasta resulting in a nested list with e.g. samples as the elements of the outer list and assigned best match for that sample for each of the multi-sequence Fastas.
    After many attempts I'm about to conclude that there's no elegant way to achieve this, but maybe I'm wrong?
    The only rather stupid-looking solution I have is to extract, as part of a workflow, each multi-sequence fasta (it's always eight of them) with __EXTRACT_DATASET__, then run vapor on each of those datasets and the list:paired collection.
    wm75 (Wolfgang Maier)
    @wm75:matrix.org
    [m]
    I can live with that if it's the only way, but don't want to build something dumb.
    Marius
    @mvdbeek:matrix.org
    [m]
    So instead of lining up collections to be processed match by match you want to do all possible combinations?
    wm75 (Wolfgang Maier)
    @wm75:matrix.org
    [m]
    yes
    Marius
    @mvdbeek:matrix.org
    [m]
    IIRC we do support that in the backend, but haven't enabled this for lack of a user interface. Just to be sure, can you share a history with your workaround ? I wonder if this could also be done by nesting your collection deeper
    wm75 (Wolfgang Maier)
    @wm75:matrix.org
    [m]
    I tried that actually, but can share, yes
    https://usegalaxy.eu/u/wolfgang-maier/h/vapor-nested-attempts
    Collections 11 and 15 are the relevant inputs.
    Lucille Delisle
    @lldelisle
    Looks too good to be true:
    image.png
    pvanheusden
    @pvanheusden:matrix.org
    [m]
    hey workflow gurus! staramr specifies species using a drop down (this is necessary to run PointFinder) - while the user could set this by changing the "default tool parameters" at pipeline invocation time, is there any way to ask for a user input parameter for the pipeline (so it shows up right at the top like other pipeline inputs) and connect this to the dropdown?
    Marius
    @mvdbeek:matrix.org
    [m]
    Yes, you can click on the add connection to module button, then connect a text parameter to that input
    It'll be shown as a select list
    Note that only works for selects, not conditionals, since conditionals can add arbitrary inputs and outputs, breaking workflows
    pvanheusden
    @pvanheusden:matrix.org
    [m]
    "add connection to module" button is the <-> ?
    Marius
    @mvdbeek:matrix.org
    [m]
    yes
    pvanheusden
    @pvanheusden:matrix.org
    [m]
    ah damn, the staramr input is a conditional - instead of making it "use pointfinder: yes / no" and then "which database", they (PHAC-NML) combined it into one
    Marius
    @mvdbeek:matrix.org
    [m]
    I think this particular conditional could be flattened by moving the unvalidated one into the main select, then checking whether or not the custom flag is needed in cheetah
    Marius
    @mvdbeek:matrix.org
    [m]
    The next workflows call is in 60 minutes:
    Workflow WG call
    Thursday, 17 November ยท 16:00 โ€“ 17:00
    Google Meet joining info
    Video call link: https://meet.google.com/myu-vozy-bsj
    Lucille Delisle
    @lldelisle
    I won't be able to join because I have another seminar at the same time but please keep me updated if you find an agreement on the multiple workflow directory.