18.01 on Kubernetes fails lifting Galaxy due to missing galaxy.yml

[pcm32]

Currently failing on k8s due to:

Waiting for database
Traceback (most recent call last):
  File "/usr/local/bin/check_database.py", line 18, in <module>
    db_url = get_config(sys.argv)['db_url']
  File "/export/galaxy-central/lib/galaxy/model/orm/scripts.py", line 126, in get_config
    properties = load_app_properties(config_file=config_file, config_prefix=config_override, config_section=config_section)
  File "/export/galaxy-central/lib/galaxy/util/properties.py", line 91, in load_app_properties
    with open(config_file, "r") as f:
IOError: [Errno 2] No such file or directory: '/etc/galaxy/galaxy.yml'

For some reason the startup process on 18.01 (master on this repo, master on galaxy-ansible-extras) fails to go past the database waiting part. It seems that is not picking up the environment variables setup for the database connection I presume... I'm not actively deleting any galaxy.yml files, so if it is not finding it, it is because it hasn't been added to the (init) container I presume...

Any thoughts @bgruening? Thanks!

[pcm32]

I had to add the following to avoid the issue:

https://github.com/galaxyproject/ansible-galaxy-extras/commit/b6c3836cae867e42b64a544692e4a24f40e64840

However is weird, because the copy is done in the docker init container:

https://github.com/bgruening/docker-galaxy-stable/blob/10789e6d6ca71051d6b98e38033e49137036c00c/compose/galaxy-init/Dockerfile#L31

I guess the issue is that contents of /etc/galaxy might not be currently copied from init to web container...

[bgruening]

mh, but the var seems to be correct: https://github.com/bgruening/docker-galaxy-stable/blob/10789e6d6ca71051d6b98e38033e49137036c00c/compose/galaxy-base/Dockerfile#L27

[bgruening]

Ah its too late. We copy this inside the init containers, but the init container only prepares the export-dir - so this can never end up in the web container if I'm not missing anything.

[pcm32]

Yes, that is what I meant on my previous comment.

[pcm32]

I have made the PR so that we can close this.... unless that you want a more proper solution (I wouldn't bother and try to work ourselves out of the init container, which would sort this issue).