| name | archive-taxonomy |
| description | Use when maintaining a local NCBI Taxonomy archive for offline lineage and taxon lookups in EDirect workflows. |
| disable-model-invocation | true |
| user-invocable | true |
archive-taxonomy
Quick Start
- Command:
archive-taxonomy [daily|-index]
- Local executable:
/home/vimalinx/miniforge3/envs/bio/bin/archive-taxonomy
- Full reference: See references/help.md for detailed usage
When To Use This Tool
- Build a local NCBI Taxonomy archive for offline taxon, lineage, and rank lookups.
- Refresh taxonomy records after the upstream taxdump changes.
- Rebuild postings so local EDirect searches can query taxonomy fields without going back to NCBI.
- Use this when you want taxonomy data to live inside the same EDirect local-archive structure as other databases.
Common Patterns
export EDIRECT_LOCAL_ARCHIVE=/data/edirect
archive-taxonomy
archive-taxonomy daily
archive-taxonomy -index
Recommended Workflow
- Set
EDIRECT_LOCAL_ARCHIVE and confirm the archive root is writable.
- Make sure the required EDirect helpers and local Go toolchain are available.
- Run
archive-taxonomy to download the taxdump and populate the local archive.
- Follow with
daily or -index as a separate command when you need refreshed search/posting layers.
- Check the
DAT, DWN, POP, IDX, INV, COL, MRG, and PST timing blocks before relying on the rebuilt archive.
Guardrails
--help and --version are not metadata-only; they still run real archive setup logic.- The script depends on
EDIRECT_LOCAL_ARCHIVE, pm-setup, pm-prepare, and a working local go compiler.
- Cleaning and indexing must be run as separate invocations.
- The cleanup ladder (
-clean, -scrub, -scour, -erase, -zap) is destructive and removes progressively more of the local taxonomy archive.
- Default FTP mode may try Aspera-backed transfer; pick
-https or -ftp explicitly if transport behavior matters.
