القائمة
Use when maintaining a local PubMed Central full-text archive for offline PMC search 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
| name | archive-pmc |
| description | Use when maintaining a local PubMed Central full-text archive for offline PMC search or bulk processing. |
| disable-model-invocation | true |
| user-invocable | true |
archive-pmc [download|verify|missing|index]/home/vimalinx/miniforge3/envs/bio/bin/archive-pmcreferences/help.md for complete usage details# 1) Download and populate the local PMC archive
export EDIRECT_LOCAL_ARCHIVE=/data/edirect
archive-pmc
# 2) Check for missing PMC packages after a failed or partial sync
archive-pmc -missing
# 3) Rebuild local search/posting structures
archive-pmc -index
EDIRECT_LOCAL_ARCHIVE and confirm the local archive root is writable.archive-pmc to fetch and populate the local archive.-verify or -missing before rebuilding postings.-index only after the local content looks complete, then inspect the timing summary for DAT, DWN, POP, IDX, INV, COL, MRG, and PST.--help and --version are not metadata-only; they still run archive setup and can emit missing-helper or missing-environment errors.EDIRECT_LOCAL_ARCHIVE, pm-setup, and pm-prepare.download, verify, missing, and index are distinct modes; use them deliberately instead of assuming a no-arg run will validate everything.-clean, -scrub, -scour, -erase, -zap) is destructive and must be run separately from -index.-stem changes the generated text index content, so record it if you need reproducible local search behavior.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.