galaxyproject / galaxyproject/galaxy

breaking refgenconf release

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Description

Hi! We just made a release of [refgenconf (v0.10.0)](https://pypi.org/project/refgenconf/) with a wide array of advancements, including using unique, sequence-derived genome identifiers (digests) instead of human-readable identifiers to refer to genomes. Users can use human-readable aliases to refer to the genomes, but under the hood, refgenconf operates on digests.

Unfortunately, this led to changing the asset directory structure, asset names, and config format, which we described in the documentation. This is a breaking release, as the old asset inventory will be no longer compatible with refgenconf v0.10.0. Users must upgrade config (run `refgenie upgrade` using CLI or `refgenconf.upgrade_config` function from within Python), which will also update the assets directory.

**Useful references:**

- [config upgrade tutorial](http://refgenie.databio.org/en/latest/config_upgrade_03_to_04/)
- [config spec](http://refgenie.databio.org/en/latest/genome_config/) (see “Upgrading the configuration file” and “Config file changelog” sections)
- [aliases usage and motivation](http://refgenie.databio.org/en/latest/aliases/)

Please let us know if you have any questions or concerns!

cc @nsheff @xuebingjie1990

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