New check_galaxy_config command to help upgrade a galaxy instance config

[julozi]

The check_galaxy_config command compare two galaxy config files (current config and new sample config) and reports new config options and deprecated options.

[jmchilton]

Thanks for the contribution - this script looks very helpful!

While useful, I'm not sure I think this belongs here in this project - but perhaps other people envision this project differently than I do. I was hoping to stick to API related functionality here. I think putting this in Galaxy core - say in scripts/ would potentially be a better home. Is there a reason you wanted to contribute it here instead of there?

Also just as a heads up, I do expect the next Galaxy version (17.09) will have YAML config options by default for Galaxy with make targets for linting the config (make config-lint and make config-validate). See galaxyproject/galaxy#3179 for the start of this idea applied to the tool shed and report application.

[julozi]

Hi @jmchilton ,
It seems that I have been misinformed ;) I was thinking that ephemeris was "an unofficial random scripts repository". I can move my script to the Galaxy core repo however if the config format is about to change, my script will be deprecated soon.
Do you think it is worth making a pull request on the galaxy core repo ?

[julozi]

Any update on this ? Should I make a pull request on the galaxy core repo instead ?

[jmchilton]

I'd like a second opinion - this is a community effort and other people may disagree with me. Ping @bgruening @mvdbeek - any thoughts on this?

[dannon]

(not one of the ones you requested specifically, but I think I'd agree -- having it in galaxyproject/galaxy in the /scripts makes more sense to me)

[bgruening]

I also think in scripts is perfect - that said I'm still not sure what belongs into this repo here and always surprised about the creativity of our community.
@julozi do you mind submit it into Galaxy core?

[mvdbeek]

Maybe we can add @jmchilton's statement from issue #2 to the Readme:
"this project is the realm for things that manage Galaxy but don't require Galaxy - management that leverages the API."

[bgruening]

@julozi can you add this script to Galaxy main?

[rhpvorderman]

@julozi Has this script been added? I think this PR can be closed.