galaxyproject / galaxyproject/brc-analytics
Pangenome: capture UCSC hub links for the 8 member assemblies
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Description
Parent epic: #1322
The "Member assemblies" table needs one link per assembly that opens the UCSC browser **with the pangenome tracks visible**. Those tracks live in the standalone **BRC pangenome hub** (`hgdownload.soe.ucsc.edu/hubs/BRC/pangenome_plasmodium_vivax_v1/`), not the default GenArk hub — so the current `ucscBrowserUrl` (`/h/`) won't show them; the link needs to attach the hub (`hgTracks?genome=&hubUrl=…/hub.txt`).
**Questions for whoever owns the hub deployment:**
- It looks like the hub **isn't deployed yet** — `…/pangenome_plasmodium_vivax_v1/hub.txt` returns 404. Is it deployed somewhere (or planned for this path), and **what is the link** to view an assembly with the pangenome tracks?
- What **track-visibility params** should the link include so the composite tracks (`brc_pangenome_chains/_annot/_select`) show by default (e.g. `&brc_pangenome_chains=full`)?
The 8 members and the UCSC assembly to target:
| Strain | UCSC hub accession |
|---|---|
| PvP01 (ref) | GCA_900093555.2 |
| **Sal-I** | **GCF_000002415.2** (GCA hub is 404; UCSC has the GCF) |
| PvW1 | GCA_914969965.1 |
| PAM | GCA_949152365.1 |
| PvSY56 | GCA_003402215.1 |
| PvT01 | GCA_900093545.1 |
| PvC01 | GCA_900093535.1 |
| MHC087 | GCA_040114635.1 |
## Acceptance criteria
- A hub-loading URL captured for each of the 8 members, each opening UCSC with the pangenome tracks visible.
- Sal-I targets `GCF_000002415.2`.
Depends on the pangenome hub being deployed (#1279).
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