Where communities thrive


  • Join over 1.5M+ people
  • Join over 100K+ communities
  • Free without limits
  • Create your own community
People
Activity
    Patrick Bovio
    @pbovio
    or can i combine bigwigs?
    to only intersect 2n fused to 3n fused??
    Helena Rasche
    @erasche
    Hi @EnzoLalli_twitter I've received your emails, we'll respond to them shortly
    Thomas Wollmann
    @ThomasWollmann
    Is there a tool to perform a post/get request directly from galaxy? It would be awsome, if I can directly send my workflow results to a REST API based archive.
    Björn Grüning
    @bgruening
    You mean sending results to Zenodo etc?
    Thomas Wollmann
    @ThomasWollmann
    for example
    Björn Grüning
    @bgruening
    we have that on our todo list
    but no progress so far :(
    Thomas Wollmann
    @ThomasWollmann
    hmm this should be relatively easy. just a simple curl if you dont care about ddos protection.
    Björn Grüning
    @bgruening
    the complicated part is the authentification I guess
    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.