القائمة
Use when maintaining a local NCBI Taxonomy archive for offline lineage and taxon lookups in EDirect workflows.
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-taxonomy |
| description | Use when maintaining a local NCBI Taxonomy archive for offline lineage and taxon lookups in EDirect workflows. |
| disable-model-invocation | true |
| user-invocable | true |
archive-taxonomy [daily|-index]/home/vimalinx/miniforge3/envs/bio/bin/archive-taxonomy# 1) Refresh the local taxonomy archive
export EDIRECT_LOCAL_ARCHIVE=/data/edirect
archive-taxonomy
# 2) Rebuild only the incremental index and invert layers
archive-taxonomy daily
# 3) Rebuild the full local taxonomy postings set
archive-taxonomy -index
EDIRECT_LOCAL_ARCHIVE and confirm the archive root is writable.archive-taxonomy to download the taxdump and populate the local archive.daily or -index as a separate command when you need refreshed search/posting layers.DAT, DWN, POP, IDX, INV, COL, MRG, and PST timing blocks before relying on the rebuilt archive.--help and --version are not metadata-only; they still run real archive setup logic.EDIRECT_LOCAL_ARCHIVE, pm-setup, pm-prepare, and a working local go compiler.-clean, -scrub, -scour, -erase, -zap) is destructive and removes progressively more of the local taxonomy archive.-https or -ftp explicitly if transport behavior matters.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.