GA2 overall design

# Overall design specs

This document outlines minimal; requirements for the first release.

## 10,000 feet overview

Here the JSON config is populated by intersecting GA species list with NCBI Datasets


The following discussion uses zebra finch as an example.

## Landing page

## Species page

Example -> https://brc-analytics.org/data/organisms

(See also https://github.com/galaxyproject/ga2/issues/13)

### Content

Use list of genomes from the UCSC VGP Hub page (e.g., https://docs.google.com/spreadsheets/d/1YuekX-rKDe6NeSHA4b5Vyn3dZsTGqVmr38fWmPFjtOQ/edit?usp=sharing)

> [!WARNING]
> The UCSC does not appear to list Alternative assemblies. E.g., look at https://hgdownload.soe.ucsc.edu/hubs/VGP/ for Zebra finch. These need to be listed.

### Look and feel

Exactly as currently at https://brc-analytics.org/data/organisms

## Genomes page

Example -> https://brc-analytics.org/data/organisms/7165

(See also https://github.com/galaxyproject/ga2/issues/12)

### Content

Displayed columns are defined in #12.

> [!NOTE]
> We need to think about how to display primary data from this page. This can be a link to rdeval summaries. Can we also provide a Galaxy-centric link like this (e.g., sending users to the current repository of primary data and give them the ability to upload data and analyze it):
>
> 

### Look and feel

## Assembly page

Example -> https://brc-analytics.org/data/assemblies/GCF_000005575_2

Review the overall design specifications and compare the referenced landing, species, genomes, and assembly pages with issues #12 and #13. Confirm the required content, including UCSC VGP assemblies and primary-data links, and clarify the unresolved design decisions before implementation; the issue does not identify files, tests, or a complete definition of done.

Written by the indexing model from the issue text.