galaxyproject / galaxyproject/brc-analytics
Pangenome: settle the permanent, BRC-owned hub URL for the P. vivax hub
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Description
Parent epic: #1322
## Problem
The *P. vivax* pangenome UCSC browser links (#1337) currently point at a **personal hubspace path**:
```
https://genome.ucsc.edu/hubspace/a6/anekrut/BRC_Pangenome_Pv_v1/hub.txt
```
This works today (verified HTTP 200), but it's Anton's personal UCSC hubspace — not a stable BRC-owned location. The issue body for #1337 originally assumed a different path (`hgdownload.soe.ucsc.edu/hubs/BRC/pangenome_plasmodium_vivax_v1/`) which 404s. Before the hub URL gets hardcoded into `build-pangenomes.ts` / `pangenomes.json` (#1341), we need to settle where the hub permanently lives.
## What to decide
- **Permanent home for the hub** — a stable BRC-owned path (e.g. an `hgdownload…/hubs/BRC/…` location) rather than a personal hubspace. Ties into the BRC Data Store hosting decision (#1326).
- **Who owns publishing/republishing** the hub to that location, and how it's refreshed when the pangenome is regenerated (#1339).
- **Clean up the hub contents** — `hub.txt` currently carries junk tracks leaked from build scripts (`build_orthogroup_bb.py`, `run_phase_k.sh`, etc.); harmless per @maximilianh but should be removed for the production hub.
- **Track-visibility defaults** — confirm the params (if any) needed so the composite tracks (`brc_pangenome_chains/_annot/_select`) show by default.
## Acceptance criteria
- A stable, BRC-owned hub URL confirmed and documented, replacing the personal hubspace path.
- The permanent URL is what #1341 hardcodes as the build constant for the `hgTracks` links.
- Owner of the publish/refresh path identified.
Depends on / relates to: #1337 (links), #1341 (build), #1326 (data store), #1339 (workflow).
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