Getting Started

Requirements

You need Git, Bash, and at least one supported runtime:

• Claude Code
• Codex CLI

Python is needed for the router, catalog generation, and some skill-local helper scripts. Development and documentation commands use uv for Python tooling.

Install

Clone the repository and install both Claude Code and Codex integrations:

git clone https://github.com/fmschulz/omics-skills.git
cd omics-skills
make install

The default install uses symlinks. That keeps the installed agents and skills in sync with the repository after git pull.

Install for only one runtime:

make install-claude
make install-codex

Use copies instead of symlinks when the checkout will not stay on disk:

make install INSTALL_METHOD=copy

Enable Routing Hints

The optional hook runs the router for each prompt and injects a short routing hint into Claude Code or Codex:

make install-hook
make hook-status

Temporarily disable the hook for one shell session:

export OMICS_SKILLS_AUTOROUTE=0

Remove the hook:

make uninstall-hook

Use an Agent

Claude Code:

claude --agent omics-scientist

Codex CLI:

codex --system-prompt ~/.codex/agents/omics-scientist.md

You can also run the router directly before choosing an agent:

python3 scripts/skill_index.py route "draft a response letter for reviewer comments"

Verify the Install

make status
make test

For more installation details and troubleshooting, use the Installation Guide.