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Cristian
@cche
Hi, I’m trying to upgrade to 18.05 (from 17.09) and when launching galaxy I get:
Ident authentication failed for user “galaxy”
The config is in the yml file and the exact same connection string is used. I start uwsgi from the command line as user galaxy or supervisor as root and the same error occurs.
Any idea how to solve this?
Tomas
@TKlingstrom
What should I look for?
Martin Cech
@martenson
it should throw an exception when it fails to create folder
so stacktrace should be in the log I think
I will test this locally
Tomas
@TKlingstrom
Great, I'll test it tonight again on my home officer computer as well.
Martin Cech
@martenson
@TKlingstrom it works for me on 18.05 locally
have you explicitly logged out and back in again?
Tomas
@TKlingstrom
I tried by using incognito mode and register a new user
any changes to your codebase compared to release?
Tomas
@TKlingstrom
Well I was running Björns Docker.
So:
docker run -d -p 8081:80 -v /home/user/galaxy_storage/:/export/ bgruening/galaxy-stable
Then I altered the code in /etc/galaxy/galaxy.yml . Changing the brand worked
So it was reading the .yml file.
Marius van den Beek
@mvdbeek
@cche is there anything before/after that message ? You don't have to switch to yml btw, you can continue using the ini file if that works for you
Tomas
@TKlingstrom
I also tried to manually create the folder userlibs2/ in galaxy-central and also a user folder with my e-mail but it was not visible in the data libraries menu
Martin Cech
@martenson
that sounds important
does galaxy have permissions to read/write there?
what is your folder structure? I think Galaxy expects the path to be relative to its root (if it is a relative path)
Björn Grüning
@bgruening
@TKlingstrom what is userlibs2/ that does not look like a path?
Martin Cech
@martenson
try using absolute paths
Tomas
@TKlingstrom
@bgruening , it was what I set the folder location to.
user_library_import_dir: userlibs2/
Björn Grüning
@bgruening
as @martenson said try a full-path - like /tmp/ or something
Tomas
@TKlingstrom
All the default options listed in the Galaxy configuration were relative paths so I thought it was the preferred option
Martin Cech
@martenson
when it works, it is, but we are debugging now
Tomas
@TKlingstrom
I'll try it tonight as soon as the kids sleep, thank you.
Tomas
@TKlingstrom
This message was deleted
Daniel Blankenberg
@blankenberg
Also hit an issue again with the uwsgi wheel on my mac, as mentioned by @mvdbeek, but i am on python 2.7.15. galaxyproject/galaxy#6470
Marius van den Beek
@mvdbeek
but for you it's pcre that's erroring out, right ?
mine's libexpat
(getting an update from brew didn't help)
galaxybot
@galaxybot
[dan] updating my brew before didn't help either, i just force installed the standard uwsgi
[dan] same sort of error as before
Daniel Blankenberg
@blankenberg
ImportError: dlopen(/Users/me/git/galaxy/.venv/lib/python2.7/site-packages/uwsgi.so, 2): Library not loaded: /usr/local/opt/pcre/lib/libpcre.1.dylib
Referenced from: /Users/me/git/galaxy/.venv/lib/python2.7/site-packages/uwsgi.so
Reason: image not found
Marius van den Beek
@mvdbeek
huh, at least for python 3 we're not even building wheels in starforge-recipes. that's a little weird
Marius van den Beek
@mvdbeek
too many environments, can't reproduce this right now
Daniel Blankenberg
@blankenberg
Does seem to be a strange outcome. At least manually installing uwsgi gets things going for me, but I can’t imagine that there is something terribly unique about my setup.
Marius van den Beek
@mvdbeek
did you try brew unlink pcre && brew link pcre ?
Daniel Blankenberg
@blankenberg
Did not, but brew info does show it as not being installed for me.
presumably manually installing it would work, but should it be required?
Marius van den Beek
@mvdbeek
no clue, seems like statically linking could be done during the build ?
Daniel Blankenberg
@blankenberg
That might be the correct thing to do.
pvanheus
@pvanheus
has anyone seen a _remove_dead_weakref error from planemo? I'm trying to test a new data manager I'm working on and hitting it (as in: https://gist.github.com/pvanheus/4269f262dfb5ccc99082cd0bcca42a88) - this is on Ubuntu 18.04 with a fresh planemo virtualenv...
this is normally something I see when I mix a conda python with a virtualenv - but there is no conda involved here...
Jennifer Hillman-Jackson
@jennaj
@martenson is this the best method? Do you want to recommend anything else? re: uploading large datasets in a local https://biostar.usegalaxy.org/p/29319/
pvanheus
@pvanheus
@jennaj they could something like the from-user-directory library import? https://galaxyproject.org/data-libraries/#from-user-folder