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skills.md

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Skills

BioMCP ships one embedded guide plus supporting reference files for agent workflows. The current workflow is:

biomcp skill
biomcp skill install ~/.claude

Read the guide

biomcp skill prints the embedded skills/SKILL.md overview. Start there if you want the current BioMCP workflow guidance without installing anything into an agent directory.

Install into an agent directory

Install the embedded skills/ tree into your agent directory:

biomcp skill install ~/.claude

Force replacement of an existing install:

biomcp skill install ~/.claude --force

The dir argument can point at an agent root such as ~/.claude, an existing skills/ directory, or a skills/biomcp/ directory. When you omit dir, BioMCP attempts supported agent-directory detection in your home directory and the current working tree, then prompts before installing when stdin is a TTY.

Install payload

Current builds install the full embedded reference tree into <agent>/skills/biomcp/, including:

  • SKILL.md
  • jq-examples.md
  • examples/
  • schemas/

Legacy compatibility note

biomcp skill list remains as a legacy compatibility alias and currently prints No skills found.

Numeric and slug lookups are also legacy compatibility paths. Commands such as biomcp skill 03 and biomcp skill variant-to-treatment currently fail with a clear not-found message and suggest biomcp skill.