How do I install the Archive Nmcds skill?

Run npx skillmds add vimalinx/archive-nmcds in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

Is Archive Nmcds safe to use?

This skill has not completed SkillMD's automated safety review yet. Capability flags: docs only. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Archive Nmcds?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Archive Nmcds free to use?

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

Who published Archive Nmcds?

vimalinx (@vimalinx) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Archive Nmcds by vimalinx — Agent Skill

Name: Archive Nmcds
Rating: 4.666666666666667 (3 reviews)
Author: vimalinx

File contents

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

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.

---name: archive-nmcdsdescription: Use when building or refreshing a local RefSeq NM CDS archive for offline accession and coding-sequence lookups.--- # 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 ```bash # 1) Download RefSeq mRNA files and rebuild the local archive content export EDIRECT_LOCAL_ARCHIVE=/data/edirect archive-nmcds ``` ```bash # 2) Force HTTPS transfer instead of the default FTP / Aspera path archive-nmcds -https ``` ```bash # 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.

Frequently asked questions