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    Björn Grüning
    @bgruening
    There are some tutrials with example data
    Dr. Hussein Al Tamimi
    @hussein_bio_twitter
    Hi all, please I need help. I have raw metagenomic reads and I have to remove human contaminants. So which tool in Galaxy can be used?.
    Praveen Kumar M
    @praveenkumarpgiindia
    @bgruening A tutorial for MD simulation of lysozyme in water is present. But an MD simulation workflow of protein and ligand together is absent. My team is working on creating a workflow. This is essential to fight against COVID-19. If anyone wishes to join our team are also welcome.
    Simon Bray
    @simonbray
    @praveenkumarpgiindia we are working on a tutorial at the moment, will share it when it is complete
    in the meantime, if you want to share your workflow we'd be happy to check it
    Praveen Kumar M
    @praveenkumarpgiindia
    @simonbray Sure i will be happy to share and get your valuable inputs
    Looking forward for your tool
    By the mean time, I have a question the merge tool which has been created is for merging itp file of ligand into top file of protein. How to merge the gro file of ligand and protein which is also a necessary part? Should we explore on creating tool itself for this ?
    Nitin Gupta
    @Nitin0304Gupta_twitter
    @simonbray I am trying to perform a molecular dynamics study of protein-ligand interaction. The merge tool in galaxy only merges the itp file of ligand into the top file of protein or is it merging the gro file of ligand into protein also ?
    dkbryant513
    @dkbryant513
    Does MimodD in Galaxy not contain the tool : MiModD Read Alignment?
    Björn Grüning
    @bgruening
    @dkbryant513 yes, either https://gitter.im/usegalaxy-eu/Lobby or better even https://help.galaxyproject.org/
    I'm the original author of MiModD and I'm reading posts in those two places regularly, but not here usually.
    @dkbryant513 for your specific last question: You can use MiModD with bowtie2 as the reads aligner as long as you follow the advice at https://sourceforge.net/p/mimodd/wiki/MiModD%20on%20public%20Galaxy%20servers/
    dkbryant513
    @dkbryant513
    @bgruening Ok, but i see the bowtie2. But i can't find it in Galaxy MimodD Tool list, not the local MimodD. Because i use the MimodD in Galaxy but local. I see the MimodD read ailgnment tool in Galaxy in this example step 1: https://mimodd.readthedocs.io/en/latest/tutorial_example1.html#ex1-step0 . Now i can not find it in same way. Thank you
    Wolfgang Maier
    @wm75
    @dkbryant513 The Read Alignment tool of the MiModD tool suite is just a bundled aligner that ships with MiModD to make life easy for users of local installs. Bowtie2, OTOH, is a very good aligner that can fully replace MiModD's bundled alignment tool, but is NOT a part of the MiModD tool suite.
    If you want to use bowtie2 in a local Galaxy you have to install it separately. Public servers, OTOH, typically have bowtie2 installed anyway, and that's why they are not offering MiModD's own aligner.
    dkbryant513
    @dkbryant513
    @wm75 Okay, I got it. Very grateful for your help!
    dkbryant513
    @dkbryant513
    I want to know if the my C.elegans WGS data.Fastq from uploaded is missing metadata? so that I decide whether I need to use MiModD Reheader to add the metadata after converting the fastq file to bam, like this step 0 in https://mimodd.readthedocs.io/en/latest/tutorial_example3.html. And, I did not sequence N2 in the experiment, so there is no N2_proof_of_principle.bam file similar to above link step 0, so do I need to use MimodD Reheader in above link step 0.

    @praveenkumarpgiindia we are working on a tutorial at the moment, will share it when it is complete

    Sharing the workflow. Made by our team with tools available. Inputs welcome

    Wolfgang Maier
    @wm75
    bowtie2 does not take bam as input format. You need to use fastq and that never has metadata. You set RG-ID and sample name in bowtie2.
    dkbryant513
    @dkbryant513
    @wm75 OK, I got it. Thank you very much
    dkbryant513
    @dkbryant513
    Hello, why can't I find SnpEff Variant effect and annotation in Galaxy? Like this link:https://sourceforge.net/p/mimodd/wiki/MiModD%20on%20public%20Galaxy%20servers/
    Wolfgang Maier
    @wm75
    dkbryant513
    @dkbryant513
    @wm75 Ok,thank you very much. I find it.
    Björn Grüning
    @bgruening
    Hi all. The university network of your region went offline a few minutes ago. We hope to be online soon, again.
    Jennifer Hillman-Jackson
    @jennaj
    Hi -- when I attempt to FTP to usegalaxy.eu at ftp.usegalaxy.eu there is a warning about an insecure connection >> Status: Insecure server, it does not support FTP over TLS. Is that the correct URL (same as shown in Upload tool at EU)? Or should a different URL be used right now? Or, avoid FTP and just use file-browsed upload?
    The login is not working because of mixing up the account credentials and FTP URL for the target server, but I wasn't sure what the proper URL was right now, or if secure FTP was enabled or not at EU. Thanks!
    Björn Grüning
    @bgruening
    Hi Jen!
    We have currently this site here for information: https://galaxyproject.eu/ftp/
    dcf1007
    @dcf1007
    Hello,
    The frontend has been extremely slow and unresponsive since Friday afternoon. Does anyone know what's happening?
    Björn Grüning
    @bgruening
    I still try to understand it, but we have a very very slow storage engine.
    I'm in contact with the local compute center to figure out if it is the storage or the network.
    dcf1007
    @dcf1007
    @bgruening Thank you very much. For what is worth, regarding storage vs network, I've realised that sometimes when the system becomes responsive, if I try to see any files (even a log) the system goes down completely again.
    Björn Grüning
    @bgruening
    yes, all read and write operations are super slow
    thanks for your feedback
    Patrick Bovio
    @pbovio
    @bgruening danke fürs Datenhochladen auf Galaxy, Ester hat mir bescheid gesagt.
    @bgruening was sind denn "optical duplicates" ?
    Björn Grüning
    @bgruening
    This is when a cluster of reads is part of two very close tiles on the flowcell.
    Patrick Bovio
    @pbovio
    @bgruening ok, and what do I do with this information? never seen before :)
    Patrick Bovio
    @pbovio
    502 ?? Galaxy down?
    Björn Grüning
    @bgruening
    should be up and running
    Patrick Bovio
    @pbovio
    get 502 every couple of min, and web page is loading for ever. Can I test my conection to the server with ping or something?
    Björn Grüning
    @bgruening
    I will look at it
    QZ1130
    @QZ1130
    Hello ,I have a simple native question:Deseq2 Error in checkForExperimentalReplicates(object, modelMatrix) . It means I must input replicates for the newest version. Right?
    If I don't have replicates for example, I can switch to the old version of Deseq2. But will be the results different between this two version?
    Björn Grüning
    @bgruening
    @QZ1130 DESeq2 always needs replicates
    you can not analyse your data with DESeq2 if you have no replicates, also not with older version of DESeq2
    Yvan Le Bras
    @yvanlebras
    I eu, hope all is ok on your side. Just see that the Wallace Shiny IT is not available anymore on eu tool list. Not urgent!
    Björn Grüning
    @bgruening
    We will exchange some hard-drive and will be back soon.
    mayurdoke6
    @mayurdoke6
    I would like to use the human Mitochondrial genome file as a reference to map fastq file. Is it possible to add the human mitochondrial genome in the database?