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Activity
    Marius van den Beek
    @mvdbeek
    RetryActionExecutor
    https://github.com/mvdbeek/galaxy/blob/67c18de7f3ae5129a57fdb4cedb5c2882332cdc2/lib/galaxy/jobs/runners/util/cli/shell/rsh.py#L68
    Milad Miladi
    @mmiladi

    @mmiladi redeployment will happen in 30min

    To add some context, this is not currently affecting me. The examples were from an end-user who got stuck since December :-D

    Björn Grüning
    @bgruening
    its happening since December?
    Milad Miladi
    @mmiladi
    I have encountered this in Sept-October at least. The user in December. For January IDK actually.
    Yvan Le Bras
    @yvanlebras
    Hi eu. Hope all is ok on your side
    I know we already discuss about the best manner to create RStudio IT with R librairies installed, through conda will be best. But thinking about that, it seems we also can install things directly from RStudio, using the R studio terminal functionality. Unfortunately (or not ;) ), 1/ the user rstudio is not sudoer and 2/ maybe this is a security issue to let people be sudoer in a IT ?
    Jorge Fung
    @jorge_fung_twitter
    Hi there, I've been trying to use SICER for peak calling on my ChIPseq data, however after loading the data I get a message in red saying SICER is not available for the genome. I have try changing the genome dataset from TAIR10 to TAIR8 (it seems SICER only works for TAIR8) but I still encounter the same problem. Any idea ?
    Mehmet Tekman
    @mtekman

    @jorge_fung_twitter Hi there, I passed on your comment to a colleague and he suggested that you don't use SICER but either use a combination of htseq-count and DESeq2, or alternatively you just use Genrich instead.

    Hope that helps

    Jorge Fung
    @jorge_fung_twitter
    @mtekman thank you very much, I will try these. Just one more thing, are these two options good for broad peak calling? or better for narrow peak detection?
    Yvan Le Bras
    @yvanlebras
    Hi eu team. Hope all is ok on you side
    I fill a form this morning for a TiaaS for a next week Tuesday training session. I was waiting for a confirmation + number of attendees.. but I don't have informations for now. Can you give me info about the fact that if in fact the training session is cancelled the reserved resourced are reallowed to the general system ?
    Mehmet Tekman
    @mtekman

    @jorge_fung_twitter (From the same colleague)

    Genrich should be good with narrow peaks. I never really tested it with ChIP seq data. But you can set in Genrich a parameter by which the tools filters peaks on a minimum peak length. DESeq2 + htseq-count depends on the regions the user provides. Another peakcaller that I actually forgot is MACS2, actually a very famous one for ChIP-Seq. MAC2 has the options for broader or narrow peaks (https://github.com/taoliu/MACS).

    Gianmauro Cuccuru
    @gmauro
    Hi @yvanlebras , yes. We don't ask you to pay the bill anyhow. :-)
    Yvan Le Bras
    @yvanlebras
    ;)
    thank you for your rapid feedback Gianmauro !
    Just I don't want to "waste" infrastructure resources
    Gianmauro Cuccuru
    @gmauro
    :+1 appreciated
    Yvan Le Bras
    @yvanlebras
    So resources allocation are made per user connected for the training, so if nobody from the training is connected, no resources is blocked ?
    Gianmauro Cuccuru
    @gmauro
    No, the resources are reserved but I can reallocate them at any time if you ask for
    Yvan Le Bras
    @yvanlebras
    ok, so I will keep you informed
    THANK YOU !!!!!
    HAve a nice end of week and excellent week-end !!!
    Gianmauro Cuccuru
    @gmauro
    :-D you too, ciao.
    Jennifer Hillman-Jackson
    @jennaj
    Can anyone else FTP to usegalaxy.eu? I've tried both "usegalaxy.eu" and "ftp://galaxy.uni-freiburg.de/".
    Different error messages for each. maybe "usegalaxy.eu" is not quite ready for FTP but the other used to work fine
    hum, perhaps is a temporary server issue. https://galaxyproject.statuspage.io/
    Jennifer Hillman-Jackson
    @jennaj
    suspect this question is about eu server -- but not confirmed yet https://help.galaxyproject.org/t/ftp-error-failed-to-retrieve-directory-listing/2937
    Mehmet Tekman
    @mtekman
    @jennaj Any luck using sftp (or lftp)? I think I recall having some issues last time I tried using pure ftp.
    Björn Grüning
    @bgruening
    Hi All. We have some filesystem issues and Galaxy is not reachable. We try to resolve this as quickly as possible.
    Björn Grüning
    @bgruening
    Galaxy is back, Thanks to our admins for fixing it so quickly.
    Omer Alkhnbashi
    @amri2k
    @bgruening thanks
    Björn Grüning
    @bgruening
    Thank Stefan on Monday :)
    Omer Alkhnbashi
    @amri2k
    will fo
    do
    now
    rgilsbach
    @rgilsbach
    Galaxy issues again? Quite slow...
    Interface and upload do not react
    Björn Grüning
    @bgruening
    mh
    I can not see anything bad at the moment
    Its probably this: https://stats.galaxyproject.eu/d/000000052/alerts?orgId=1&from=1581370303169&to=1581371598065&fullscreen&panelId=59
    I will look into it
    but it seems to be normal again
    Björn Grüning
    @bgruening
    @rgilsbach better?
    rgilsbach
    @rgilsbach
    Interface reacts - upload does not work...
    rgilsbach
    @rgilsbach
    ends with "adding to history" forever????
    Björn Grüning
    @bgruening
    I have it
    its again our network device
    sorry, but bedtime for you
    I can not fix this now