Genome build names, variations, metadata, GUI help

galaxyproject / idc

Simon's Data Club - Reference data for Galaxy servers

MIT License

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Genome build names, variations, metadata, GUI help #7

Open jennaj opened 5 years ago

jennaj commented 5 years ago

Linking this over here so we don't forget about it:

https://github.com/galaxyproject/tools-iuc/issues/2435

Came up a Gitter today, too. Let's try to make it less confusing going forward. I'm not stuck on how -- just that we expose the info to users.

https://gitter.im/Galaxy-Training-Network/Lobby?at=5d116902492f010bcab4b9da

natefoo commented 5 years ago

Things to decide:

Metadata
- Location: In a file next to the sequence file; what about non-sequence data?
- Format (e.g. yaml)
- Spec (required, optional keys): date fetched/built, hashes, build system basic specs, doi, references, upstream "version" (if any); what about for non-sequence data?
- Interaction with tool data tables, loc files
UI
- How do you access metadata and download the actual reference data/indexes?: link on tool form, special reference data metadata tool, data library view
- Generating references of workflow should also include references of reference data

bernt-matthias commented 5 years ago

Would like to see taxid (or similar) in the metadata.
Also wondering if there are standard metadata formats that could/should be used

dfornika commented 5 years ago

I've been experimenting with using bagit to include checksums of all files installed by a data manager. I've implemented it in this data manager for mob_suite using bagit-python.

The CWLProv and ResearchObject projects also use bagit, maybe there could be some opportunity for compatibility there?

bwlang commented 5 years ago

would also be good to include the command line and tool versions (conda version numbers?) used to generate the index in the metadata