القائمة
Use when building or refreshing a local RefSeq NM CDS archive for offline accession and coding-sequence lookups.
التثبيت باستخدام Codex أو Claude انسخ هذا Prompt والصقه في Codex أو Claude أو مساعد آخر ليراجع صفحة Skill ويثبّتها لك.
استنادا إلى تصنيف SOC المهني
| 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.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.