菜单
Use when maintaining a local NLM NLP concept archive over PubMed for offline chemical, disease, gene, or GeneRIF lookups.
用 Codex 或 Claude 帮你安装 复制这段 Prompt，粘贴到 Codex、Claude 或其他助手里，让它检查 Skill 页面并帮你完成安装。
基于 SOC 职业分类
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-nlmnlp |
| description | Use when maintaining a local NLM NLP concept archive over PubMed for offline chemical, disease, gene, or GeneRIF lookups. |
| disable-model-invocation | true |
| user-invocable | true |
archive-nlmnlp [daily|-index]/home/vimalinx/miniforge3/envs/bio/bin/archive-nlmnlp# 1) Refresh the local NLM NLP extras and archive over HTTPS
export EDIRECT_LOCAL_ARCHIVE=/data/edirect
archive-nlmnlp -https
# 2) Rebuild only the incremental index and invert layers
archive-nlmnlp daily
# 3) Rebuild merged postings for downstream local searching
archive-nlmnlp -index
EDIRECT_LOCAL_ARCHIVE and confirm the archive root exists and is writable.pm-setup, pm-prepare, and the local Go toolchain are available.archive-nlmnlp or archive-nlmnlp -https to stage the latest PubTator / GeneRIF support files.daily or -index as a separate command when you need refreshed postings.DWN, IDX, INV, MRG, and PST timing blocks to confirm each stage actually ran.--help and --version are not safe inspection switches; they still trigger archive setup and prerequisite checks.EDIRECT_LOCAL_ARCHIVE, pm-setup, pm-prepare, and a local go compiler.-https or -ftp explicitly if you need predictable transfer behavior.