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Use when building or refreshing a local RefSeq NM CDS archive for offline accession and coding-sequence lookups.
Install with Codex or Claude Copy this prompt, paste it into Codex, Claude, or another assistant, and let it review the skill page and install it for you.
Based on SOC occupation classification
Use when joint-genotyping one or more germline gVCFs into a cohort VCF with GATK GenotypeGVCFs.
Use when running GATK HaplotypeCaller to emit per-sample germline variant calls or gVCFs from analysis-ready BAM/CRAM inputs.
Use when splitting mixed accession-like text into one lowercase token per line in EDirect-style text pipelines.
Use when converting ACE assembly files into SAM while preserving legacy ACE-specific padded or contig-sequence behavior.
Use when pretty-printing tab-delimited output with left, center, right, or decimal-aware numeric alignment in EDirect text workflows.
Use when masking columns or coordinate ranges in multiple-sequence alignments before downstream HMMER or alignment-processing steps.
| 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 [-index|-clean|-scrub|-scour|-erase|-zap]/home/vimalinx/miniforge3/envs/bio/bin/archive-nmcdsreferences/help.md for complete documentation# 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
EDIRECT_LOCAL_ARCHIVE and confirm the archive root is writable.archive-nmcds to stage source files, generate accession/CDS tables, and populate the archive.-index as a separate follow-up step when you need refreshed search/posting structures.-clean, -scrub, -scour, -erase, or -zap only when you truly need to tear down stale layers before rebuilding.--help and --version are not metadata switches here; they still walk through setup, download, and generation code paths.EDIRECT_LOCAL_ARCHIVE, pm-setup, and pm-prepare to be available.-clean removes incremental/index state, while -zap removes the source records and the remaining archive tree.