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Activity
    davelopez (David López)
    @davel0pez:matrix.org
    [m]
    You should be able to continue :) but uploads or some jobs could take some more time to catch up
    tingting081
    @tingting081
    ok, thanks. I will try to continue. Those jobs haven been waiting for running for a few hours. Just no idea about when it will start running.
    thank you so much for your help.
    gmauro
    @gmauro:matrix.org
    [m]
    We have currently, ~2000 uploads jobs running and ~3000 waiting in the queue. We are trying some tuning to speed up the queue
    tingting081
    @tingting081
    Got it. Much appreciated for your help and consideration.
    Surbhigrewal
    @Surbhigrewal
    Hi Is there any way to upload using a URL from Microsoft Sharepoint?
    bgruening
    @bgruening:matrix.org
    [m]
    is the URL public accessible?
    daikez
    @daikez
    any problems with usegalaxy.eu? couldn't load up data since yesterday.
    irisbeirith
    @irisbeirith_twitter
    no, all good for me with usegalaxy.eu. However, I do regularly open the page in a new tab again to access all.
    ZhouHY-77
    @ZhouHY-77
    Hi guys, I uploaded some FASTA files, but they are always grey in history. Do you know how to make them available? Thank you a lot!
    irisbeirith
    @irisbeirith_twitter
    Hi guys, anyone knowing the tool for SRA data import in FASTA format? I can only find the one for FASTQ. Thanks in advance
    bgruening
    @bgruening:matrix.org
    [m]
    You want to have reads in FASTA format? I don't think they store it that way. But you can convert fastq to fasta.
    irisbeirith
    @irisbeirith_twitter
    I tired to convert from Fastq to Fasta. however, the result is not matching with Mirdeep ( I'm trying to follow galaxy tutorial for miRNA analysis). SRA does provide an option to directly download in Fasta, but I can't find an option here, unfortunately.
    Patrick Bovio
    @pbovio
    @bgruening:matrix.org Hi Björn, I get an "Internal Server Error" when trying to export a history into a workflow. Any insides? I would like to export all tools and settings to the workflow to publish it alongside a Revised Manuscript.
    there used to be a simple .xml format for this
    bgruening
    @bgruening:matrix.org
    [m]
    @pbovio: can you try again, but let me know when you hit the button?
    Patrick Bovio
    @pbovio
    hitting in 5 sec
    again in 5 sec @bgruening:matrix.org
    bgruening
    @bgruening:matrix.org
    [m]
    I think I have it
    thanks
    Patrick Bovio
    @pbovio
    I also tried other histories
    bgruening
    @bgruening:matrix.org
    [m]
    Seems that davelopez (David López) already has a fix. We need to deploy it.
    it will work tomorrow latest
    Patrick Bovio
    @pbovio
    ok cool
    and how about the xml file it used to produce?
    to have it text searchable?
    bgruening
    @bgruening:matrix.org
    [m]
    it was a JSON I think
    and you still get those if you create a workflow
    Patrick Bovio
    @pbovio
    I just want it to document what I did on e.g. GitHub
    bgruening
    @bgruening:matrix.org
    [m]
    once you have a worklow you can download the workflow as a txt file - in JSON format
    Patrick Bovio
    @pbovio
    ok, I'll give it a look tomorrow and get back to you
    thanks Björn
    bgruening
    @bgruening:matrix.org
    [m]
    ok, thanks!
    Hope you are doing fine! Long time ... :)
    Patrick Bovio
    @pbovio
    Oh, I have important news for you ;) -> PM
    Patrick Bovio
    @pbovio
    @bgruening:matrix.org I tried the "Extract Workflow" funktion again. Still "Internal Server Error"
    pvanheusden
    @pvanheusden:matrix.org
    [m]
    I have a collection of many samples that I ran fastp on (on .eu) - some jobs failed with the cryptic error message "Unable to finish job" and nothing in stderr. What is the easiest way to select all the failed datasets and re-run them to see if they succeed a second time?
    bgruening
    @bgruening:matrix.org
    [m]
    There is an API to restart all failed jobs in a history and it's in bioblend
    If that does not work you need to reload all failed jobs and click rerun inplace
    pvanheusden
    @pvanheusden:matrix.org
    [m]
    ok I'll try bioblend
    pvanheusden
    @pvanheusden:matrix.org
    [m]
    I'm trying to help out a colleague who is doing Galaxy 101 but one of their jobs failed with the message "Unable to finish job". This is history ID 0876ff39fabc4ccd - is there something wrong with the server?
    I just tried re-running the job and got a new error - "cat: write error: Broken pipe" - this is an error reported in the stderr (whereas the previous one had empty stderr) but again it looks strange to me
    pvanheusden
    @pvanheusden:matrix.org
    [m]
    I am trying to move a history from usegalaxy.eu to usegalaxy.org. I exported on .eu and have a link, but when I try and use that to import to .org I get a 403: Forbidden error. is there some setting I am meant to change to make the exported link accessible?
    bgruening
    @bgruening:matrix.org
    [m]
    Are jobs still crashing?
    pvanheusden
    @pvanheusden:matrix.org
    [m]
    yes.. "cat: write error: Broken pipe"
    pvanheusden
    @pvanheusden:matrix.org
    [m]
    seems to be specific to this tool though?
    pvanheusden
    @pvanheusden:matrix.org
    [m]
    ok, looks like this was two different errors, with one masking the other.
    the original error was "Unable to finish job" - then when that went away the "cat: write error: Broken pipe" showed up. The second error is happening with version 1.0.1 of the "Show beginning1" tool but "text_processing/tp_head_tool" version 1.1.0 - the tool that should be used for the Galaxy 101 tutorial - works
    both tools are, however, called "Select first lines from a dataset".
    bgruening
    @bgruening:matrix.org
    [m]
    Ah ok