bio-ncbi-datasets-cli

92 / 100 · Low risk

Fine to try. Some of what it can do is expected: a data skill usually connects to databases or online services with your credentials.

By lilinji/GeneTind-Life-Skills (GitHub) · data · 17 stars · scanned at commit 908229c

Download genome assemblies, gene records, and ortholog data from NCBI using the modern Datasets v2 CLI (replaces assembly_summary.txt scraping and many EFetch workflows). Use when bulk-pulling genome assemblies, gene metadata across species, ortholog sets, or BLAST databases; when E-utilities are too slow for genome-scale work; or when automatic checksum verification, parallel download, and clean accession-driven retrieval are required. Encodes the JSON-lines output format, dataformat conversio…

Works with any agent that supports SKILL.md skills.

What this skill can do

Runs commands on your computer

The author does not mention this.

Found in 9 places.

skills/bio-ncbi-datasets-cli/SKILL.md, line 32conda install -c conda-forge ncbi-datasets-cli
skills/bio-ncbi-datasets-cli/SKILL.md, line 94datasets summary genome taxon "Escherichia coli" --reference --as-json-lines \
skills/bio-ncbi-datasets-cli/SKILL.md, line 128datasets download genome accession GCF_000001405.40 \

Show 6 more

skills/bio-ncbi-datasets-cli/SKILL.md, line 146datasets download genome taxon Bacteria \
skills/bio-ncbi-datasets-cli/SKILL.md, line 164datasets summary gene symbol BRCA1 \
skills/bio-ncbi-datasets-cli/SKILL.md, line 176datasets summary gene symbol BRCA1 --taxon human --ortholog --as-json-lines \
skills/bio-ncbi-datasets-cli/SKILL.md, line 186datasets summary genome taxon "Salmonella enterica" \
skills/bio-ncbi-datasets-cli/SKILL.md, line 206out = subprocess.run(cmd, capture_output=True, text=True, check=True)
skills/bio-ncbi-datasets-cli/SKILL.md, line 214subprocess.run(cmd, check=True)

Sends data to these websites: ftp.ncbi.nlm.nih.gov

This is disclosed by the author in the skill's SKILL.md or README. Expected for a data skill.

Found in 1 place.

skills/bio-ncbi-datasets-cli/SKILL.md, line 35curl -O https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v2/linux-amd64/datasets

Install

Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.

if [ -e ~/.agents/skills/'bio-ncbi-datasets-cli' ] || [ -L ~/.agents/skills/'bio-ncbi-datasets-cli' ]; then echo 'A skill folder named bio-ncbi-datasets-cli already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/lilinji/GeneTind-Life-Skills' "$d" && git -C "$d" checkout --quiet '908229c955510a1841b216e8bf58f6b22818d4dc' -- 'skills/bio-ncbi-datasets-cli' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/bio-ncbi-datasets-cli' ~/.agents/skills/'bio-ncbi-datasets-cli' && rm -rf "$d"; fi

Codex reads ~/.agents/skills directly. For Claude Code, Cursor, Copilot, Gemini CLI, Antigravity or OpenCode, also link it. For Claude Code: ln -s ~/.agents/skills/'bio-ncbi-datasets-cli' ~/.claude/skills/'bio-ncbi-datasets-cli' (other agents: ~/.cursor/skills, ~/.copilot/skills, ~/.gemini/skills, ~/.gemini/config/skills, ~/.config/opencode/skills). Or install through the finder skill, which does both.

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Score history

Date	Version	Score
2026-11-11	`908229c`	92