wrong permissions on /galaxy/upload_store

[tdudgeon]

Using the latest tag on Docker hub I got into the situation when I was getting this error in the logs:

DEBUG:galaxy.containers:config file './config/containers_conf.yml' does not exist, running with default config
Traceback (most recent call last):
  File "lib/galaxy/webapps/galaxy/buildapp.py", line 49, in app_factory
    app = galaxy.app.UniverseApplication(global_conf=global_conf, **kwargs)
  File "lib/galaxy/app.py", line 67, in __init__
    self.config.check()
  File "lib/galaxy/config.py", line 842, in check
    self._ensure_directory(path)
  File "lib/galaxy/config.py", line 827, in _ensure_directory
    raise ConfigurationError("Unable to create missing directory: %s\n%s" % (path, e))
ConfigurationError: Unable to create missing directory: /galaxy/upload_store
[Errno 13] Permission denied: '/galaxy/upload_store'

The /galaxy dir is owned by root. By creating the /galaxy/upload_store dir and changing the ownership to galaxy.galaxy made the problem go away, but the /galaxy dir is ephemeral so the issue will recurr.

Should the /galaxy dir be chown'ed to galaxy.galaxy in the Dockerfile and is there good cause to symlink it under /export?

[bgruening]

Thanks to @jyotipm29 we are back on track :smile: The new 24.1 image contains a lot of changes and reflects the latest developments in Galaxy. I would like to close this PR, but please feel free to reopen and rebase against the latest version.

Please give it a try:

docker run -p 8080:80 -p 8021:21 -p 4002:4002 --privileged=true -e "GALAXY_DESTINATIONS_DEFAULT=slurm_cluster_docker"   -v /tmp/galaxy-data/:/export/ quay.io/bgruening/galaxy:24.1

... or any other combination. The readme has been updated. Please add any useful tip to it.

For a list of changes, see the Changelog.