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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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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

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.

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