القائمة
Use when maintaining a local PubMed XML archive for offline literature search, indexing, or bulk processing.
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
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.