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Use when maintaining a local PubMed XML archive for offline literature search, indexing, or bulk processing.
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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-pubmed |
| description | Use when maintaining a local PubMed XML archive for offline literature search, indexing, or bulk processing. |
| disable-model-invocation | true |
| user-invocable | true |
archive-pubmed [download|verify|missing|index]/home/vimalinx/miniforge3/envs/bio/bin/archive-pubmed# 1) Download new PubMed files and populate the local archive
export EDIRECT_LOCAL_ARCHIVE=/data/edirect
archive-pubmed
# 2) Check which PubMed packages are missing locally
archive-pubmed -missing
# 3) Rebuild the local PubMed search/posting structures
archive-pubmed -index
EDIRECT_LOCAL_ARCHIVE and confirm the archive root is writable before starting.archive-pubmed to download new files and populate the archive.-verify or -missing if the refresh was interrupted or you suspect archive gaps.-index only after the data files are stable, then inspect the timing summary before using the local archive with other EDirect tools.--help and --version are not safe inspection switches; they still run archive setup and can emit real helper/env failures.EDIRECT_LOCAL_ARCHIVE, pm-setup, pm-prepare, and pm-refresh.-clean, -scrub, -scour, -erase, and -zap are destructive maintenance modes and must be run separately from -index.-zap or -scour in some stale-data scenarios.-stem and -strict change how text is normalized and indexed, so record them in reproducible workflows.