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 for skills and Claude agents. Codex agents are rendered as TOML, so rerun the installer after changing an agent prompt.

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

Ask Codex to delegate to omics-scientist, or mention an installed skill such as $bio-annotation. Codex discovers the generated subagent definitions in ~/.codex/agents/.

You can also install the native plugin from this checkout:

codex plugin marketplace add .
codex plugin list --available --json
codex plugin add omics-skills@omics-skills

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.