| name | archive-nmcds |
| description | Use when building or refreshing a local RefSeq NM CDS archive for offline accession and coding-sequence lookups. |
| disable-model-invocation | true |
| user-invocable | true |
archive-nmcds
Quick Start
- Command:
archive-nmcds [-index|-clean|-scrub|-scour|-erase|-zap]
- Local executable:
/home/vimalinx/miniforge3/envs/bio/bin/archive-nmcds
- Full reference: See
references/help.md for complete documentation
When To Use This Tool
- Build a local RefSeq NM mRNA/CDS archive for offline accession-driven sequence work.
- Generate the master accession list and CDS offset table that EDirect uses during local archive population.
- Refresh local RefSeq source records, then rebuild index and posting layers for offline lookups.
- Repair or reset broken archive state with the staged cleanup levels when a rebuild is required.
Common Patterns
export EDIRECT_LOCAL_ARCHIVE=/data/edirect
archive-nmcds
archive-nmcds -https
archive-nmcds -index
Recommended Workflow
- Set
EDIRECT_LOCAL_ARCHIVE and confirm the archive root is writable.
- Ensure the supporting EDirect helper commands are present before starting a rebuild.
- Run
archive-nmcds to stage source files, generate accession/CDS tables, and populate the archive.
- Use
-index as a separate follow-up step when you need refreshed search/posting structures.
- Reach for
-clean, -scrub, -scour, -erase, or -zap only when you truly need to tear down stale layers before rebuilding.
Guardrails
--help and --version are not metadata switches here; they still walk through setup, download, and generation code paths.- The script needs
EDIRECT_LOCAL_ARCHIVE, pm-setup, and pm-prepare to be available.
- Cleanup levels are hierarchical and destructive:
-clean removes incremental/index state, while -zap removes the source records and the remaining archive tree.
- Cleaning and indexing must be separate invocations.
- Archive generation creates accession and CDS-offset side tables, so allow time and disk space beyond the raw downloads.
