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https://usegalaxy.eu status: https://stats.galaxyproject.eu Forum: https://help.galaxyproject.org

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Repo info

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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

thinking about http://book.orthanc-server.com/users/rest.html

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

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

Björn Grüning

@bgruening

have you tried: https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/bgruening/diffbind/diffbind/2.6.6.4

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?

Björn Grüning

@bgruening

@Sayantani89_gitlab you mean this one? https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.0.2.0

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.

https://usegalaxy.eu/tool_runner?tool_id=__FILTER_FROM_FILE__ and https://usegalaxy.eu/tool_runner?tool_id=__APPLY_RULES__

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

Björn Grüning

@bgruening

@mmiladi done

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