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Use when maintaining a local NCBI Taxonomy archive for offline lineage and taxon lookups in EDirect workflows.
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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-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.