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    akankshabafna
    @akankshabafna
    @gmauro:matrix.org : Could you help me , @beatrizserrano has email correspondence with me since last year and as I have received OOO from her I am reaching out to the group.
    gmauro
    @gmauro:matrix.org
    [m]
    Have you purged deleted datasets from your histories? Have you verified if you can process your data in batches?
    akankshabafna
    @akankshabafna
    I have purged in the past. I can try again , but I got some new NGS following from my previous and will like to have 500 GB space top up to start .
    gmauro
    @gmauro:matrix.org
    [m]

    I have purged in the past. I can try again ...

    Do it on regular basis, have been allocated to you a not usual amount of space, and it's your duty to using it responsibly.

    akankshabafna
    @akankshabafna
    @gmauro:matrix.org Noted. Done , still need more space to run my jobs.
    gmauro
    @gmauro:matrix.org
    [m]
    I still see 232 datasets on your histories that have to be purged.
    akankshabafna
    @akankshabafna
    @gmauro:matrix.org Which history are yo referring to? I just purged deleted datasets from all histories.
    gmauro
    @gmauro:matrix.org
    [m]
    Fine. I will take care of your request and let you know.
    akankshabafna
    @akankshabafna
    @gmauro:matrix.org Many Thanks
    Sona Charles
    @charles_sona_twitter
    I have just started to work on metagenomics. I have been following the 16S Microbial Analysis with Mothur tutorial. I would like to work with SILVA 138_1 fasta files for alignment. I wanted to know from where I can get the file since the one used in the tutorial is V4. Thank you.
    hexylena
    @hexylena:matrix.org
    [m]
    probably user error, but i'm having trouble viewing PDFs in the center panel in galaxy? the js console shows _iframeChangeHandler error
    works in scratchbook / own tab though.
    khalomar1
    @khalomar1
    I follow this Galaxy training called "Age prediction using machine learning", and in the ""Analyze RNA-seq dataset" II use this tool "Ensemble methods for classification and regression", and I have this error An error occurred with this dataset:
    This job was resubmitted to the queue because it encountered a tool detected error condition on its compute resource.
    {'selected_tasks': {'header': True, 'prediction_options': {'prediction_option': 'predict'}, 'selected_task': 'load'}}
    OMP: Info #212: KMP. It works fine with the "Analyze DNA methylation dataset".
    bgruening
    @bgruening:matrix.org
    [m]
    @Serekh2_twitter: can you please submit an error report?
    Piniel kambey
    @pinielkambey_gitlab
    Hi, can some one assist me on "where and how to start analysing my single cell RNA data" I have 10x genomics data.
    Björn Grüning
    @bgruening
    And bookmark this site :)
    Piniel kambey
    @pinielkambey_gitlab
    Thanks @bgruening , but i still need a video describing these steps in single cell analysis (perhaps a hands on recording)
    bgruening
    @bgruening:matrix.org
    [m]
    Why would you need a video?
    Piniel kambey
    @pinielkambey_gitlab
    Easy to understand @bgruening
    Björn Grüning
    @bgruening
    @pinielkambey_gitlab please understand that creating a video is a lot of work
    and is very frequently outdated
    Please spent a few minutes to look at the resources we provide, there are even Videos linked for you
    but you need to spent some time and energy to at least look at the material :)
    bgruening
    @bgruening:matrix.org
    [m]
    If you follow the linkd videos you will also find: https://www.youtube.com/playlist?list=PLNFLKDpdM3B_mZjY3UF0qaDgjgIqNi7Tb
    Piniel kambey
    @pinielkambey_gitlab
    Thank you @bgruening
    lgallegovillar
    @lgallegovillar
    Hi there,
    When creating a workflow using collections (in my case I have multiple treatments A, B, C, D, E… Control) sometimes I need to select a few samples from the list of results (for example a condition to compare treatment A vs Control) as input for the next tool in the workflow. How can I deal with this? . Is there any way to select from the list (results of tool1) only specific tags (Treatment A and Control) as input for the next tool2? Thank you in advance for your support:)
    @lgallegovillar I guess this tutorial will help
    lgallegovillar
    @lgallegovillar
    @bgruening:matrix.org Thanks :) it works quite well with DESeq2 but I guess it only works with those tools that allow to put group tags as input, is this correct? Or is there a way to make group tags as input data available for any tool in general?
    wm75 (Wolfgang Maier)
    @wm75:matrix.org
    [m]
    lgallegovillar (lgallegovillar) I think you can achieve what you want with Filter List or Extract dataset both in Collection Operations, which let you cut down a collection to just elements with predefined names.
    Adrian Zimmer
    @ZimmerA
    @bgruening We're having a problem with one of our tools: https://usegalaxy.eu/root?tool_id=proteomiqon_peptidedb
    When we try to start a job, we get the error: proteomiqon-peptidedb: command not found
    Local testing still works, the tests on the galaxyp repo also seemed to have executed fine.
    If you have time, it would be awesome if you could help us with this. :)
    bgruening
    @bgruening:matrix.org
    [m]
    I will have a look later today. Looks like a missing conda env
    Is your new tool installed?
    Adrian Zimmer
    @ZimmerA
    Awesome, thanks!
    Everything else is perfect so far. We're currently testing our workflow in production.
    bgruening
    @bgruening:matrix.org
    [m]
    Awesome!
    Thanks a lot @ZimmerA
    Adrian Zimmer
    @ZimmerA
    https://usegalaxy.eu/root?tool_id=proteomiqon_psmstatistics also has the "command not found" issue
    bgruening
    @bgruening:matrix.org
    [m]
    @ZimmerA: can you please try again
    Adrian Zimmer
    @ZimmerA
    @bgruening:matrix.org Yes! Works perfect, thank you very much :)
    bgruening
    @bgruening:matrix.org
    [m]
    Awesome!
    Rock on!
    Adrian Zimmer
    @ZimmerA
    Yeah :D Thanks again for all of the support
    M Bernt
    @bernt-matthias
    Is it a bug in the dada2 tools or in usegalaxy.eu that the image in the help is not shown: https://usegalaxy.eu/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fdada2_learnerrors%2Fdada2_learnErrors%2F1.20%2Bgalaxy0
    bgruening
    @bgruening:matrix.org
    [m]
    In Eu
    Could not figure out what the problem is so far
    But wasn't a priority ...
    lgallegovillar
    @lgallegovillar
    @wm75:matrix.org Thanks a lot Wolfgang for your suggestions, I will test soon.
    Bérénice Batut
    @bebatut:matrix.org
    [m]
    Thanks a lot for all the work to make usegalaxy.eu running all the time! Happy sysadmin day gmauro Helena Rasche ❤️
    1 reply