archive-nmcds

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

# 1) Download RefSeq mRNA files and rebuild the local archive content
export EDIRECT_LOCAL_ARCHIVE=/data/edirect
archive-nmcds

# 2) Force HTTPS transfer instead of the default FTP / Aspera path
archive-nmcds -https

# 3) Rebuild incremental index, invert, merge, and postings layers
archive-nmcds -index

Recommended Workflow

1. Set EDIRECT_LOCAL_ARCHIVE and confirm the archive root is writable.
2. Ensure the supporting EDirect helper commands are present before starting a rebuild.
3. Run archive-nmcds to stage source files, generate accession/CDS tables, and populate the archive.
4. Use -index as a separate follow-up step when you need refreshed search/posting structures.
5. 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.