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Julien Seiler
@julozi
@erasche thanks for this feedback
my concern was about user geeting confused and trying to register on every subdomains… but you are right, most of them will certainly stick on the subdomain they are used to use… I think I will try the PR anyway and keep talking with our usegalaxy « steering comitee » about this subject
Helena Rasche
@erasche
sounds good!
yeah, I really need to do something to indicate on subdomains that "you can login with your .eu credentials here"
but I guess the real solution is that everyone uses elixir AAI
and it won't matter as much
Julien Seiler
@julozi
talking about Elixir AAI, do you know if there is a way to avoid FB/Google registration ? We would like AAI to be limited to academic users only.
Helena Rasche
@erasche
Then you need to request the bona fide attribute
But consider that you will exclude e.g. all freiburg university users, because our uni still hasn't federated with elixir.
Julien Seiler
@julozi
Damned… I always though that « academic users only » policy was challenging on the technical point of view...
Helena Rasche
@erasche
It is, and not for sensible reasons like "what is the definition of an academic", but instead for ridiculous ones like taking forever to federate.
Martin Cech
@martenson
@erasche what does æfederate' mean here?
sofialumc
@sofialumc
Hello!I am completely a beginner with bioinformatics, and in desperate need of help! I have a BAM file with genomic coordinates and I would like to convert them in transcript coordinates, is there an easy way to do that without the need to realign to the transcriptome?
Helena Rasche
@erasche
@martenson usually university library / group in charge of university identities/local authentication, needs to federate with elixir. Which can take some time with bureaucracy, or if ldap attributes don't align and things must be added/removed/changed/etc.?
Martin Cech
@martenson
oh, so something like linking related accounts together?
Gildas Le Corguillé
@lecorguille
I though that Elixir AAI was including Edugain ?
Agathe Nkouawa
@ankouawa_gitlab
Hello, my galaxy was frozen and I closed it. Now I cannot open it again. I received this message: GURU MEDITATION: #a3ae13dd4b43414ab023df3f3d028f21
Internal Server Error
that is the message that I received

Internal Server Error
Galaxy was unable to successfully complete your request

An error occurred.
This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem.

The error has been logged to our team. If you want to contact us about this error, please reference the following

GURU MEDITATION: #3d69df44e2314164b179ffb14233f24f

Martin Cech
@martenson
@ankouawa_gitlab is this 'your' Galaxy as in your server, or are you working on usegalaxy.org?
usegalaxy.org is currently upgrading, so there is some expected downtime happening
Agathe Nkouawa
@ankouawa_gitlab
yes
i am using usegalaxy.org
do you think it is just the downtime?
Martin Cech
@martenson
@ankouawa_gitlab in that case please try again later.
it is the downtime for sure
Agathe Nkouawa
@ankouawa_gitlab
alright. Thank you
Martin Cech
@martenson
https://status.galaxyproject.org/ will tell you when the server is up
Agathe Nkouawa
@ankouawa_gitlab
thank you
Brad Langhorst
@bwlang
i’m seeing a strange loop on our local galaxy:
[WorkflowRequestMonitor.monitor_thread] Workflow invocation [86834] scheduled
it’s repeating this every few seconds over and over.
any ideas?
galaxybot
@galaxybot

[unknown]
unable to login [Uncategorized]
Hello.

I am trying to login and get data using ‘usegalaxy.org’.

However, I was not able to login and get message as ‘Uncaught exception i…

galaxybot
@galaxybot
[unknown]
upload from FTP gives: bad request (400) [usegalaxy.org support]
hi there, I uploaded to usegalaxy.org some fasta files with mozilla, but when I click to start the import of those file in the ‘choose FTP f…
Martin Cech
@martenson
@bwlang with galaxyproject/galaxy#8664 you could troubleshoot it maybe
lumin2003
@lumin2003
Hi I am trying to reset my password. But I cannot. Uncaught exception in exposed API method was showing.
Martin Cech
@martenson
@lumin2003 thanks for the report, we'll look into it
Which Galaxy server? It works for me on usegalaxy.org
lumin2003
@lumin2003
I tried several times
Brad Langhorst
@bwlang
thanks @martenson , I’ll check that out. a restart resolved it.
Peter Truong
@iampetertruong_twitter

Hi there, I'm trying to use galaxy via usegalaxy.org (from Australia), but am unable to do any work. I submitted several jobs yesterday (mapping RNA-seq data) but woke up to find that the majority of the jobs paused. I tried re-executing the jobs today but am unable to do so (i have adequate disk space). The error I'm getting is "Internal Server Error
Galaxy was unable to successfully complete your request
GURU MEDITATION: #deed739d563b46639a3adf729c587892"

I checked the status of the galaxyproject and it looks like the server is up but I'm still having issues.

Thank you

galaxybot
@galaxybot

[unknown]
Cannot login UseGalaxy.org Server (Main) [usegalaxy.org support]
Hi! I cannot load the usegalaxy page. An error message would occur as follow:

Internal Server Error

Galaxy was unable to successfully compl…

galaxybot
@galaxybot
[unknown]
Galaxy down.... [Uncategorized]
When will Galaxy be back up and running? Its been down since yesterday.
Wolfgang Maier
@wm75
I'm trying to install tools from the toolshed into my local Galaxy (release_19.05) and keep getting: tool_shed.util.hg_util ERROR 2019-09-19 15:14:10,584 [p:22844,w:1,m:0] [uWSGIWorker1Core3] Error cloning repository: Command '['hg', 'clone', '-r', u'13', u'https://toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar', u'/home/wolma/galaxy_19.05/database/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/850f3679b9b4/rgrnastar']' returned non-zero exit status 255 Output was: abort: connection ended unexpectedly
tried with various tools and with main and test toolshed
strangely I can install data managers though
Is this a problem with the toolsheds or with my Galaxy configuration?
John Chilton
@jmchilton
The Galaxy test cases are failing on CI with the same error - I don't think it is you
Wolfgang Maier
@wm75
Good to know - thanks!
Jennifer Hillman-Jackson
@jennaj
Galaxy Main https://usegalaxy.org status: We did a software update yesterday at that took a bit longer than expected. Then there was another problem earlier today and a few hiccups continue.
The current status is always here: https://galaxyproject.statuspage.io/
Expand the Galaxy Main section to review status. Hover over the block for the day to see details and sometimes a link with more information. Right now, this is the message: https://galaxyproject.statuspage.io/incidents/07my40spgd4c
galaxybot
@galaxybot

[unknown]
bowtie2 not working [usegalaxy.org support]
hi all, I’m trying to align some fasta using bowtie2 but I get the error:

tool error

An error occurred with this dataset:

Unable to finis…