New genome+annotation set: Glycine max, Jidou 17 (JD17)

[StevenCannon-USDA]

Main steps for adding new genome and annotation collections

Genus/species/collection names:

What are the collection types and names? Example:

• /Glycine/max/genomes/JD17.gnm1.TW7L

• Glycine/max/annotations/JD17.gnm1.ann1.CLFP

• Add collection(s) to the Data Store -- currently at /usr/local/www/data/annex/Glycine/max

• Validate the README(s)

• Update about_this_collection.yml

• Calculate AHRD functional annotations

• Calculate gene family assignments (.gfa)

• Add to pan-gene set

• Load relevant mine

• Add BLAST targets

• Incorporate into GCV

• Update the jekyll collections listing -- automatic for SoyBase when Data Store metadata submodule is updated

• Update browser configs -- automatic for SoyBase when Data Store metadata submodule is updated

• run BUSCO

Adding to the watch group: @maxglycine @jd-campbell @sammyjava

[adf-ncgr]

@StevenCannon-USDA I think I briefly mentioned in separate email but I think the actions on here that impact the data representation (ie AHRD/gene family assignment) are complete so it can be moved from annex to regular datastore whenever you see fit (unless @sammyjava wants to do a pre-validation regarding issues that the loader would pick up). I'll mention that I got a bit confused about the relationship of this genome to our other JiDouNo_17 from the Liu et al 2020 pangenome. My guess is that it is probably the same elite Chinese line tackled by two independent groups. I suppose we have precedent for not treating it as gnm2 of that accession from cases like Wm82_IGA1008, and since it seems they decided to abbreviate this to JD17 that should be enough to keep them distinguishable in contexts where the key gets dropped. Anyway, I think the remaining actions on the list can proceed once it's in place in the official datastore location...

[sammyjava]

Go ahead and move to regular DS, I don't normally look at stuff in the annex. If there are issues you'll hear about them. I'm post-processing GlycineMine now, anyway, so it'll be long time before I add this accession.

[StevenCannon-USDA]

Have moved this to the public DS.