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Activity
    Helena Rasche
    @hexylena:matrix.org
    [m]
    we left the UI based upload running and it failed very unhelpfully have ~90 minutes.
    tamannasharma22
    @tamannasharma22
    uploading data from link showing error invalid HTML tags ...can anyone help
    wm75 (Wolfgang Maier)
    @wm75:matrix.org
    [m]
    @tamannasharma22: do you have access rights to the data behind that link, i.e. can you down load it with your browser without being logged in into an account on the remote server? The error usually means that the remote server responded with some html-formatted error message instead of sending data.
    tamannasharma22
    @tamannasharma22
    yes i am using ncbi link....then also it is giving same error
    wm75 (Wolfgang Maier)
    @wm75:matrix.org
    [m]
    can you share the failing NCBI link here?
    tamannasharma22
    @tamannasharma22
    wm75 (Wolfgang Maier)
    @wm75:matrix.org
    [m]
    @tamannasharma22: well, that is an html page (look at its source code in your browser) so what Galaxy will receive when you give it that link is the html code, not the data you want.
    You either need to locate the underlying data directly at NCBI and get e.g. an ftp link to it, or simpler use this tool https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.7+galaxy0 to download it using its ID.
    Helena Rasche
    @hexylena:matrix.org
    [m]
    <del>Is Apply Rules working for others?</del> nvm, eu nonresponsive.
    gmauro
    @gmauro:matrix.org
    [m]
    should be back in ~1 min
    Helena Rasche
    @hexylena:matrix.org
    [m]
    super :)
    platuconsina
    @platuconsina
    A job using Count.seqs tool from Mothur still waiting to run, since yesterday update. Someone could help. Thanks!
    gmauro
    @gmauro:matrix.org
    [m]
    @platuconsina: Mothur tools run on a different/tiny cluster and there is always a long queue. Nothing wrong here
    platuconsina
    @platuconsina
    Great :)
    ToMatschulla
    @ToMatschulla
    Hi, I was using the single cell tutorial with scanpy and I´m also interested in trajectory contruction. With which dataset should I go into the jupyter pipeline? Thx
    mtekman
    @mtekman:matrix.org
    [m]
    @ToMatschulla: For the Jupyter analysis in Galaxy, the Trajectory Analysis using Python training is recommended, and it uses a pre-clustered scRNA dataset from this Zenodo link
    ToMatschulla
    @ToMatschulla
    And what would be the input file from the tutorial ( Clustering 3K PBMCs with Scanpy )?
    mtekman
    @mtekman:matrix.org
    [m]
    @ToMatschulla : Oh sorry, the input is the AnnData object and the iPynb from the above Zenodo link, specifically:
    https://zenodo.org/record/4726927/files/Trajectories_Instructions.ipynb
    https://zenodo.org/record/4726927/files/Final_cell_annotated_object.h5ad
    ToMatschulla
    @ToMatschulla
    but when I run one of the single cell tutorials listed in the training material which file from that can I use for further processing the trajectory tutorial? Or are there additional steps to do before using it for trajectory analysis?
    mtekman
    @mtekman:matrix.org
    [m]

    @ToMatschulla : Oh I see! Yes, so I think as long as you have an AnnData file which has some prior-clustering on it, then you should be able to use that in the trajectory analysis.

    For example, I think the AnnData file you generate from the Plant Training should be able to be used in the Trajectory training linked above, and also the output of the "Clustering 3K PBMCs" training should produce an AnnData file you can use for trajectory analysis too.

    ToMatschulla
    @ToMatschulla
    ok, I will look into these, thank you for the help
    Pablo G Goicoechea
    @pgoikoetxea
    Hi, I guess i need some help to transfer data between galaxy.org and galaxy.eu. I shared te history with the data in galaxy.org, but when trying to import into galaxy.eu I jus get an error (data contain HTML content)
    Pablo G Goicoechea
    @pgoikoetxea
    Wendi Bacon
    @nomadscientist
    I’m having problems with Jupyter Notebooks - when we go to run a fresh notebook with no files, it just says ‘waiting to run’ indefinitely, and never actually makes a notebook to access from the Interactive tools page.
    Helena Rasche
    @hexylena:matrix.org
    [m]
    you at the quota?
    gmauro
    @gmauro:matrix.org
    [m]
    Hi @nomadscientist it could happen
    we don't have infinite resources
    Wendi Bacon
    @nomadscientist
    No, still 47% and also there are two of us and she is super new...
    Helena Rasche
    @hexylena:matrix.org
    [m]
    how many notebooks are you running currently?
    gmauro
    @gmauro:matrix.org
    [m]
    and IT are quite demanded
    Wendi Bacon
    @nomadscientist
    her one, me currently 2, trying two different ways
    gmauro
    @gmauro:matrix.org
    [m]
    but probably I can manually free some slots, let me see
    ten slots freed, you are on run
    1 reply
    yes
    we 10 nodes with ~10 slots each, dedicated to ITs
    Helena Rasche
    @hexylena:matrix.org
    [m]
    gmauro
    @gmauro:matrix.org
    [m]
    and users, currently, can run no more than 5 ITs
    1 reply
    Wendi Bacon
    @nomadscientist
    Yes yes, both worked, I’ve now closed them both down to keep slots free. That is FASCINATING. So basically, if universal Galaxy users don’t close/delete their Interactive tools, we’re hosted...
    1 reply
    Helena Rasche
    @hexylena:matrix.org
    [m]
    i can kill an rstudio.
    gmauro
    @gmauro:matrix.org
    [m]
    after 30 days, they will be killed anyway
    Wendi Bacon
    @nomadscientist
    This is really important to know, as we were aiming to make more R / Python tutorials, but if it’s going to wreck Galaxy, maybe not...
    gmauro
    @gmauro:matrix.org
    [m]
    but if can suggest nicely to kill them if not used, would be great
    1 reply
    Helena Rasche
    @hexylena:matrix.org
    [m]
    this was why the old system killed after inactivity
    1 reply
    not just letting them run forever
    nope. now they run until min(30 days, killed)
    annagias
    @annagias
    any idea why unique.seqs fails after galaxy update?
    Björn Grüning
    @bgruening
    do you have an error report
    annagias
    @annagias
    it says dataset have been resumbitted or sth like that
    but i haven't done anything
    and the parameters are the same as I would run this job successfully in the past
    annagias
    @annagias
    Please help! When I am running unique.seqs the job fails saying "This job was resubmitted to the queue because it encountered a tool detected error condition on its compute resource." Is this a bug or can I fix it somehow?