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mtruglio
@mtruglio

some more interesting elements:

  • all the tools installed from the standard toolshed work fine. No problems there, their environments are recognized as such.
  • if I exclude the install_tool_deps instruction from the dockerfile, and I run it in a container afterwards, it complains about permissions, and suggests to chown -R 1450:1450 /tool_deps/_conda/pkgs/cache
  • If I actually execute chown -R 1450:1450 /tool_deps/_conda/pkgs/cache then install_tool_deps starts working fine, and the environments it creates (identical to the non-working ones from before), work fine.

I would say this is a permissions issue. Somehow the mulled environments -which are installed after the startup-lite instruction, are not available to the galaxy user 'admin' for activation.

Björn Grüning
@bgruening
But than you can change the user in your dockerfile before executing RUN install_tool_deps -
the easiest way would be probably to upload your tools to the ToolShed again
mtruglio
@mtruglio
hmm ok. What should I write in my Dockerfile to change user?
Björn Grüning
@bgruening
USER galaxy
mtruglio
@mtruglio
ok let me try this. Thanks a lot, much appreciated
image.png
meanwhile: changing owner to the already installed - and not working - mulled environment folder, makes it work again. So yes, it's just a matter of installing dependencies as 'galaxy' and not root.
mtruglio
@mtruglio
so, the problem with USER galaxy is that if I insert it before startup-lite, it gets stuck on "Waiting for database" forever.
but install_tool_deps needs a running server in order to work. Ideas?
ifubar (ross lazarus)
@ifubar:matrix.org
[m]
perhaps add USER root where you need docker to switch back to acting as root?
mtruglio
@mtruglio
yeah, but the issue here seems to be this:
  • install_tool_deps needs to be run as galaxy user in order to create the envs with the correct ownership
  • install_tool_deps also needs a running startup_lite in order to work, a galaxy server at localhost:8080 must be alive somehow.
  • Unfortunately, startup_lite needs to be launched while acting as root, otherwise it gets stuck on 'waiting for database'
so I cannot find a way to launch install_tool_deps while a galaxy server is alive
(as non-root)
Björn Grüning
@bgruening
@mtruglio you can also just add your chmod/chuser to the Dockerfile after you have installed your tools
mtruglio
@mtruglio
yep, that's what I'm trying now :)
mtruglio
@mtruglio
Ok so it seems that the smartest way to solve this is to run chgrp -R galaxy /tool_deps/_conda/envs && chmod g+s -R /tool_deps/_conda/envs just after startup_lite. This way, all the envs that will be placed in that folder will inherit the galaxy group ownership. Running chmod/chuser after the installation of all the dependencies would have worked as well, but it would be excruciatingly long.
Björn Grüning
@bgruening
:+1:
Jennifer Hillman-Jackson
@jennaj
Question at the lobby. The build is older and there are some similar existing issue tickets plus the chat above seems to be related. I'll point them back here. https://gitter.im/galaxyproject/Lobby?at=61527e14a41fd20699b24c1a includes a link to an issue ticket bgruening/docker-galaxy-stable#587
Steven Shum
@shenweiyan
I have tried to install docker-galaxy-stable, however, there is a problem that doesn't work correctly, it seems docker galaxy cannot start normally, does anyone know how to solve this problem? Thank you. bgruening/docker-galaxy-stable#587
Kenzo52YZ
@Kenzo52YZ
@shenweiyan tried to answer you
by the way it seems like this issue has been encountered by many before trying to use different systems to run the docker image
Steven Shum
@shenweiyan
@Kenzo52YZ Thank you for your reminder.
Edgar F
@gad83
the package https://wheels.galaxyproject.org/simple/futures/futures-3.1.1.tar.gz
seems to be causing an issue : bgruening/docker-galaxy-stable#588
is it possible we are supposed to use the other one: https://wheels.galaxyproject.org/simple/futures/futures-3.1.1-py2-none-any.whl
can we add a condition in the file requirements.txt to determine when to use eachpackage?
Steven Shum
@shenweiyan
Hi everyone,
I have developed some tools locally and packaged them in my docker. Does anyone know how to run my own docker on galaxy-docker?
Thank you in advance.
Jennifer Hillman-Jackson
@jennaj
1 reply
Jennifer Hillman-Jackson
@jennaj
Another Galaxy Help question. The person is trying to implement expanded login authentication methods. https://help.galaxyproject.org/t/unable-to-activate-google-oidc-login/7910