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gget — Claude Code skill: what it does, how to install

Bioinformatics skill providing unified access to over 20 genomic databases via CLI and Python. Useful for gene lookups, alignments, and protein structure downloads.

Install into Claude Code · Skills CLI (Vercel) All methods and platforms ↓ 
npx skills add K-Dense-AI/scientific-agent-skills --skill gget -a claude-code
Open on GitHub

What gget does

gget provides a single interface to 24 modules across 6 genomic categories. It retrieves gene metadata from Ensembl, fetches structures from PDB or mmCIF, and queries disease associations through OpenTargets and COSMIC. CLI queries return JSON by default or CSV with the -csv flag, while Python returns dictionaries or DataFrames.

The tool requires network access, Python 3.12 or newer, and gget==0.30.8. Both alphafold and gpt modules are deprecated upstream. Local MUSCLE and DIAMOND commands break without compatible binaries and OpenMP libraries on your host system. Open Targets filters run locally after the row cap, and expression data only pulls the initial page up to 3000 rows.

What it helps with

  • retrieve gene annotations and sequences from Ensembl
  • fetch protein structures in PDB or mmCIF formats
  • run local protein alignments via DIAMOND
  • query disease and drug associations in OpenTargets

Example prompts for the agent

  • Look up gene details using gget info and export them to CSV.
  • Download the mmCIF structure file for a protein using gget pdb.
  • Run multiple sequence alignment on these FASTA records using gget muscle.

How to install gget

1Skills CLI (Vercel)

npx skills add K-Dense-AI/scientific-agent-skills --skill gget -a claude-code

2Manually: put the files in place

~/.claude/skills/gget/SKILL.md

Copy the whole skill folder; for one project use .claude/skills/gget/

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Questions about gget

How to install gget in Claude Code?

Run npx skills add K-Dense-AI/scientific-agent-skills --skill gget -a claude-code. You also need Python 3.12 or higher with gget==0.30.8 installed in your virtual environment.

What databases does gget support?

It connects to over 20 bioinformatics resources. Supported sources include Ensembl, COSMIC, OpenTargets, PDB, CELLxGENE, and 8cube.

What extra setup is required for local alignments?

Running diamond or muscle locally requires compatible binary executables and OpenMP libraries installed on your machine. Modules like elm, cbio, and cellxgene require running gget setup <module> first.

See also

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