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    Helena Rasche
    @erasche
    I'm currently not super keen on the idea of "anyone can make a request as if it comes from usegalaxy.eu"
    Thomas Wollmann
    @ThomasWollmann
    you can pass the login data into the url?
    Helena Rasche
    @erasche
    surely the better UX would also be targeted tools that do specific uploads to specific services
    Thomas Wollmann
    @ThomasWollmann
    would also be happy if have this feature just on my private server
    Björn Grüning
    @bgruening
    ideally this would work with OpenID connect, imho
    @ThomasWollmann but even to your private server you need to pass in credentials, correct?
    Thomas Wollmann
    @ThomasWollmann
    yes
    just a few rest apis support openid
    Björn Grüning
    @bgruening
    @ThomasWollmann how is authentification handled at orthanc?
    This tool does upload of data with OpenID https://usegalaxy.eu/?tool_id=genomespace_exporter&version=0.0.6
    (not working at the moment, as we do not have OpenID support yet, but such a tool exists, if you need a template)
    Thomas Wollmann
    @ThomasWollmann
    if uses HTTP Basic Auth
    Ghost
    @ghost~5772e7e2c2f0db084a206e1b
    Just a heads up, dragging files into the upload box doesn't work on .eu
    Ghost
    @ghost~5772e7e2c2f0db084a206e1b
    also the upload of .xlslx doesn't work, as reported by @yvanlebras , this seems to be a specific problem of .eu -- maybe the datatype_conf.xml.sample file hasn't been updated ?
    for reference this was fixed in galaxyproject/galaxy#6867
    Helena Rasche
    @erasche
    uh
    re 6867, yes, we are not on 18.09 yet, so of course we don't have that patch yet.
    Thanks for the heads up @mvdbeek, but @yvanlebras should retry on wednesday after we've updated :)
    Schulz_Lab
    @EddaSchulz
    Hi, I cannot find the Mageck Tools any more. I would to redo some analyses. Thanks for your help.
    marbrunet
    @marbrunet
    Hi, it seems that all (most of) the proteomics tools cannot be found anymore. Was this planned? And how long before they're back? Thanks :)
    Björn Grüning
    @bgruening
    On it .. sorry
    Not planned, thats for sure :)
    marbrunet
    @marbrunet
    Thanks a lot :)
    Helena Rasche
    @erasche
    Hi @marbrunet we've fixed the issue. Sorry for the inconvenience!
    Patrick Bovio
    @pbovio
    I need a sudgestion how and at what stage I can normalise the readcounts (sequencing depth) of different "n" in ChIP-seq
    better on the .BAM or at the .bigwig level?
    Björn Grüning
    @bgruening
    if BAM -> bigwig is a straight conversion this should not matter
    but deeptools often normalizes from BAM -> bigwig already
    Patrick Bovio
    @pbovio
    I am not talking about ChiP to Input normalisation but from one ChIP/Input n to other ChIP/Input n
    seperat runs
    Patrick Bovio
    @pbovio
    I would love to use diffbind, but I have 3 n ctrl and 2 n treated and for what I understand Diffbind can only handle equal x and y
    worst case I don't use one n from ctrl and discard it but I would like to avoid it
    Patrick Bovio
    @pbovio
    @bgruening i saw there is the option to "Collapse Collection" which I love !!! But is there a way of decollaps a collection into single files again? without donwloading and uploading again?
    Yvan Le Bras
    @yvanlebras

    Thanks for the heads up @mvdbeek, but @yvanlebras should retry on wednesday after we've updated :)

    Thanks @erasche and @mvdbeek ! I will do it, but ITM I have fix the error on my personal server ;)

    Sayantani Bhattacharjee
    @Sayantani89_gitlab
    Hi, I couldnot find the bamcorrelate option in the tools. is it under some other name or is there any similar tool?
    Patrick Bovio
    @pbovio
    Hi, is it posible to remove one of 3 entrys in a colection? I have an outlying .bigwig wich I want to remove from a bamCompare collection??
    Helena Rasche
    @erasche
    There are a couple of collection operations which you can use: there is the filter collection tool and the apply rules to collection tools, both of which might let you do this.
    Neither of them I find to be extremely convenient, but these are the only options currently.
    Patrick Bovio
    @pbovio
    Ok, ill give it a try thank you
    Patrick Bovio
    @pbovio
    is Jupyter Notebook not availible at the moment?
    Loading the interactive environment failed, please contact the Galaxy administrator for assistance
    Helena Rasche
    @erasche
    No, unfortunately not
    It will be back in 2019 though
    We're currently overhauling how interactive environments launch since .org and .eu have some special restrictions we need to work around
    Patrick Bovio
    @pbovio
    Ok thank you
    Milad Miladi
    @mmiladi
    Dear admins, would u please install the latest version (0.4) of this tool. https://toolshed.g2.bx.psu.edu/repository?repository_id=771107948507dbf1 Thanks