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esg-epfl-apc / tools-astro

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DESI and PhotoZ are not appearing on the Galaxy instance? #145

Open volodymyrss opened 3 days ago

volodymyrss commented 3 days ago

@dsavchenko could you please check? At least DESI should be simple.

dsavchenko commented 2 days ago

It's a cluster-wide issue that affects the bot...

dsavchenko commented 2 days ago

DESI is affected by https://github.com/oda-hub/nb2workflow/issues/208

dsavchenko commented 2 days ago

PhotoZ requires astrorama conda channel, but we only use conda-forge in Galaxy

volodymyrss commented 2 days ago

PhotoZ requires astrorama conda channel, but we only use conda-forge in Galaxy

On private instance, you can add astrorama, right?

dsavchenko commented 2 days ago

On private instance, you can add astrorama, right?

Yes, right. I can add it if really needed

volodymyrss commented 2 days ago

On private instance, you can add astrorama, right?

Yes, right. I can add it if really needed

Please do, to test. Then maybe we migrate to conda-forge.

dsavchenko commented 2 days ago

DESI is affected by oda-hub/nb2workflow#208

But see comment there. It looks like DESI can't be easily added to Galaxy because it needs custom astroquery.

volodymyrss commented 2 days ago

DESI is affected by oda-hub/nb2workflow#208

But see comment there. It looks like DESI can't be easily added to Galaxy because it needs custom astroquery.

@Andrei-EPFL , could you change to code of the notebook so that it does not depend on custom astroquery? Just take out the code from within custom astroquery module.

dsavchenko commented 2 days ago

Please do, to test.

Well, I've just realised, the main issue with PhotoZ is PhosphorosTable input type. It's not yet supported and requires dedicated development

volodymyrss commented 2 days ago

Please do, to test.

Well, I've just realised, the main issue with PhotoZ is PhosphorosTable input type. It's not yet supported and requires dedicated development

Can you treat it as json-encoded string field? This should be a fallback for all parameters derived from StructuredParameter . I imagine some development to treat it as string, but not nearly as extensive specialized as that in MMODA.

Andrei-EPFL commented 1 day ago

@dsavchenko I have adapted the environment.yml and added a "package" desi.py file in order to replace the github code. In addition, I have also added a galaxy_help.md file in the repository https://gitlab.renkulab.io/astronomy/mmoda/desi-legacy-survey . what would be the next step to make it go on galaxy?

dsavchenko commented 21 hours ago

what would be the next step to make it go on galaxy?

We need to merge https://github.com/oda-hub/nb2workflow/pull/209 first