Where communities thrive


  • Join over 1.5M+ people
  • Join over 100K+ communities
  • Free without limits
  • Create your own community
People
Activity
    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?
    Click on the Vis button. Do you see then UCSC?
    Tomas
    @TKlingstrom
    The db was set
    But I realise that there is a blue field above the list of icons
    Facepalms
    So it is a small design change with the visualisation button leading to the "Visualize" menu but with a blue bar at the top with the links which used to be on the datasets. So it is me not used to design changes :P
    Thanks
    Miguel Angel Hernandez
    @miangher
    Hi everybody, I am currently performing an assembly process of a genome produced with reads from the nanopore system. I already performed the assembly using Flye, then the polishing using medaka, which gives me a consensus.fasta sequence. I am trying to get a corrected and chromosome level assembly using ragtag software. First I did the correction, then the scaffold, then the patch, and now I am trying to do the merge. Here in this last step I have the problem, because it does not generate any output result. I tried to use these programs directly on my computer, but I get a message : Fri Sep 23 11:11:26 2022 --- VERSION: RagTag v2.1.0
    Fri Sep 23 11:11:26:26 2022 --- WARNING: This is a beta version of ragtag merge
    Fri Sep 23 11:11:26 2022 --- CMD: ragtag.py merge ragtag.patch.fasta ragtag.patch.agp ragtag.patch.ctg.agp ragtag.patch.rename.agp
    Fri Sep 23 11:11:26 2022 --- WARNING: Without '-u' invoked, some component/object AGP pairs might share the same ID. Some external programs/databases don't like this. To ensure valid AGP format, use '-u'.
    Fri Sep 23 11:11:26 2022 --- INFO: Building the scaffold graph from the AGP files
    Traceback (most recent call last):
    File "/home/sequenceur/miniconda3/bin/ragtag_merge.py", line 430, in.
    main()
    File "/home/sequenceur/miniconda3/bin/ragtag_merge.py", line 362, in main
    agp_multi_sg.add_agps(agp_list, in_weights=weight_list, exclusion_set=comp_exclusion_set)
    File "/home/sequenceur/miniconda3/lib/python3.9/site-packages/ragtag_utilities/ScaffoldGraph.py", line 606, in add_agps
    for ap in self._get_assembly_points(agp, weight):
    File "/home/sequenceur/miniconda3/lib/python3.9/site-packages/ragtag_utilities/ScaffoldGraph.py", line 513, in _get_assembly_points.
    raise RuntimeError("{} is in {} but not {}.".format(agp_line.comp, agp, self.components_fasta_fname))
    RuntimeError: seq00000005 is in /home/sequenceur/genome_assembly/Lguyanensis_filtree/RagTag/patch/ragtag_output/ragtag.patch.agp but not ragtag.patch.fasta.
    Now I use galaxy to try to solve this problem, but apparently the result is the same. Can you please guide me?