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    bgruening
    @bgruening:matrix.org
    [m]
    Cool!
    Thats nice to hear :)
    Tito Montenegro
    @biotemon
    Where can I see the workload in realtime or usegalaxy.eu. I am loading a couple of small datasets from Zenodo and it is stalled in yellow forever. Thanks
    Tito Montenegro
    @biotemon
    Is it normal that a job stays for too long in gray? I am trying to run XCHEM TRANSFS
    bgruening
    @bgruening:matrix.org
    [m]
    @biotemon: https://stats.galaxyproject.eu/d/000000004/galaxy I guess you mean this link?
    Jobs in gray might be normal depending on how many users are running jobs currently. However in your case I think transfs is a GPU tool, so here it will take even longer ... we do not have that many GPUs
    1 reply
    Tito Montenegro
    @biotemon
    Sorry I keep asking. I get this error when running MSCONVERT. What can I do? ln: failed to create symbolic link 'qExactive01819.raw': Permission denied
    pvanheusden
    @pvanheusden:matrix.org
    [m]
    bgruening - I need to share a history with you - this is the one where when I select multiple datasets it does not give me the option to build a collection. Please DM me the correct email to share with.
    btw I tried to get an "overview" of this history using parsec but parsec -g usegalaxyeu datasets get_datasets --history_id 46051bf8534e30b9 gives me an empty list
    Anthony Bretaudeau
    @abretaud:matrix.org
    [m]
    Hi all! Would it be possible to run the interproscan data manager on usegalaxy.eu? the database is missing for latest version 5.55-88.0
    Wendi Bacon
    @nomadscientist
    Hmm… my galaxy history won’t let me download an IPYNB file from my history to my computer, I keep getting:
    {"err_msg":"Could not get display data for dataset: _serve_raw() got multiple values for argument 'headers'","err_code":500001}
    Wendi Bacon
    @nomadscientist
    Hmmm… the Interactive Jupyter Notebook seems to be struggling in general. It keeps disconnecting (Python 3 | Disconnected) and won’t run anything on the notebook. Help?
    bgruening
    @bgruening:matrix.org
    [m]
    @nomadscientist: I will look at it
    1 reply
    not sure I can do this tm, but I will try
    amini1573
    @amini1573
    Hello
    I used Import Annadata and loom to process my single cell data
    My genes file included 28 thousand gene symbols and ensemble IDs
    Now, although the output of this tool is green, the number of genes is considered zero
    And in the matrix he created, my genes are not there
    what is the reason?
    1 reply
    bgruening
    @bgruening:matrix.org
    [m]
    @amini1573: this is hard to say from your description. Did you follow any tutorial?
    Did you mapped against the correct reference genome?
    What was your mapping statistic?
    Anthony Bretaudeau
    @abretaud:matrix.org
    [m]
    hey! it seems like usegalaxy.eu/apollo is down, could someone restart it?
    bgruening
    @bgruening:matrix.org
    [m]
    mh
    Anthony Bretaudeau
    @abretaud:matrix.org
    [m]
    yeah some things are showing, but the right panel ui doesn't load for me, usually it means there's out of memory errors or things like that
    do you have access to the logs?
    bgruening
    @bgruening:matrix.org
    [m]
    I have now access to the box
    PML-research
    @PML-research
    Hi everyone, our allotted server is pmlgenomicsworkshop, with the specs of 225 GB ram and 28 cores but still the BWA is taking more than usual.
    bgruening
    @bgruening:matrix.org
    [m]
    @PML-research: I don't see many BWA in the queue.
    and there are only 4 people in your training group registered
    maybe the persons have not clicked the TIaaS link?
    One BWA job from one person in your TIaaS group is still waiting for one input dataset to be finished
    PML-research
    @PML-research
    Thank you so much for your response, but it is giving 502 error, can anyone assist in this regard please.
    bgruening
    @bgruening:matrix.org
    [m]
    Do you still see this?
    irisbeirith
    @irisbeirith_twitter
    hi team, if I want to compare total miRNA expression with one specific genes RNA expression - what would be the best workflow?
    5 replies
    irisbeirith
    @irisbeirith_twitter
    giving it a try: anyone knowing a tool for small rna binding site prediction (miRNA in my case) in human? so, equivalent to targetFinder?
    Wendi Bacon
    @nomadscientist
    Hmm… I’ve been waiting a solid 40 minutes for an (empty) Jupyter Interactive Tool to launch… is something going on with the server?
    bgruening
    @bgruening:matrix.org
    [m]
    Wow, there are a bunch of people that are running Phinch
    we have 100 of Phich Its running
    Mobina Darabi
    @mobinadarabi:matrix.org
    [m]
    hi
    if I wanna compare miR expression in cancer tissue vs normal its better to analysis miseq or rna-seq?
    pvanheusden
    @pvanheusden:matrix.org
    [m]
    where is the configuration for this site: https://africa.usegalaxy.eu/ ?
    1 reply
    pvanheusden
    @pvanheusden:matrix.org
    [m]
    thanks, seems right
    irisbeirith
    @irisbeirith_twitter
    is there a tool for expression based unsupervised gene clustering? or other types of gene expression clustering if not?
    irisbeirith
    @irisbeirith_twitter
    my data is loading since Friday for DEXSeq ... could anyone maybe check if it got stuck or if it still running ?
    2 replies
    pabanga
    @pabanga
    Hello! Is it possible to do md5 checksum on Galaxy? If so, how coulld I do it?
    pvanheusden
    @pvanheusden:matrix.org
    [m]
    hahaha thank you for reminding me that I should write that tool (there is a checksum tool in the toolshed but it does sha256, not md5). I actually need a tool to do md5 and as far as I know it is not possible in Galaxy at the moment.
    Niko Pinter
    @npinter
    Hi all, is it possible to create a collection of uploaded files within a workflow (which tool if there is one)? Is the "Apply rules" tool functional as a workflow tool? I want to build a workflow for uploaded paired-end RNAseq data and automate the rule-based generation of a paired collection.
    bgruening
    @bgruening:matrix.org
    [m]
    Yes apply rules is workflow enabled
    one of the turotials in GTN has something for that
    Niko Pinter
    @npinter
    ty!
    Tomas
    @TKlingstrom
    Where have the "display at UCSC main/test" link" on datasets gone?
    I am prepping for running the "Introduction to Genomics and Galaxy" tutorial and I realise that the bed-file datasets no longer have such a link. on the Usegalaxy.eu server.
    bgruening
    @bgruening:matrix.org
    [m]
    Are you sure you have the dbkey set?