I used to run the galaxy-stable container (on Ubuntu) with an export folder mapped to an external drive. Now, I have moved to a different computer, attached the external drive and tried to start the container mapping the same folder as the export folder. However, the container does not start and the postgresql database does not initialize (spawn error, “could not connect to database”). Can anyone help?
The original and new were both sourced from here, correct? Docker Hub
This is the directory listing: Galaxy Docker - Galaxy Community Hub
It links to this release log: GitHub - bgruening/docker-galaxy-stable: Docker Images tracking the stable Galaxy releases.
Some admin changes were introduced in the latest release. Maybe you were running an earlier release on your old computer, but installed the latest on your new computer? And that is creating a conflict? Maybe try installing the version you had originally, then upgrade? (just a guess)
There is a Gitter (or Matrix) chat for help with the Galaxy Docker container if you need more help. I’ll post for help there, and they may reply here or there. Plus, feel free to join the chat – the version(s) of the container and the Ubuntu installs would probably help with troubleshooting.
Gitter: bgruening/docker-galaxy-stable - Gitter
Matrix: Follow the link at Gitter to to the room and join to post
Let’s start there
(Have also replied in the Galaxy Gitter - bgruening/docker-galaxy-stable - Gitter)
Having a quick read of the problem, I’m going to assume you’re moving from one Ubuntu machine to another one. My gut feeling is that there might be some underlying differences between the machines and the way the external drive is mounting.
Check that you can read/write into other folders on your external drive on the new machine. If not, it sounds like an I/O error and you’ll need to have a dig into the mounting side of things.
Otherwise, see if you can read/write into the external drive, log into the container and make sure you can run some basic
bash commands. If you can do that, make sure PostGreSQL fires up and you can create new databases.
(Sorry I can’t dig into the problem any more right now)