Menu
Use when maintaining a local NLM NLP concept archive over PubMed for offline chemical, disease, gene, or GeneRIF lookups.
Install with Codex or Claude Copy this prompt, paste it into Codex, Claude, or another assistant, and let it review the skill page and install it for you.
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-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.