:whale::bar_chart::books: Docker Images tracking the stable Galaxy releases.
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_depsinstruction 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/cachethen 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.
the easiest way would be probably to upload your tools to the ToolShed again
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.
but
install_tool_deps needs a running server in order to work. Ideas?
perhaps add
USER root where you need docker to switch back to acting as root?
yeah, but the issue here seems to be this:
install_tool_depsneeds to be run asgalaxyuser in order to create the envs with the correct ownershipinstall_tool_depsalso needs a runningstartup_litein order to work, a galaxy server at localhost:8080 must be alive somehow.- Unfortunately,
startup_liteneeds 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)
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.
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
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
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?
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?
Galaxy Help question -- advice appreciated! https://help.galaxyproject.org/t/galaxy-does-not-start-database-error/7333
1 reply
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