Install¶

The pack installs from a checkout with make, or as a plugin for Claude Code or the Codex CLI. Claude Code reads the Markdown agents; Codex reads TOML agents rendered at install time.

Requirements¶

Git, GNU Make, and Python 3.11 or newer. The installer uses only the Python standard library.
Claude Code, the Codex CLI, or both.
uv or Pixi for skill helper scripts, which declare their own dependencies.

Install from a checkout¶

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

make install builds the routing catalog, links every skill into ~/.agents/skills, links the Claude agents, and renders the Codex agents.

Command	Effect
`make install-claude` or `make install-codex`	Installs for one runtime.
`make install INSTALL_METHOD=copy`	Copies instead of linking, for a checkout that will not stay on disk.
`make install LINK_CLIENT_SKILLS=no`	Leaves `~/.claude/skills` and `~/.codex/skills` untouched, for hosts where another tool manages them.
`make install-selected SELECTED_AGENT_FILES="omics-scientist.md" SELECTED_SKILL_DIRS="bio-logic bio-annotation"`	Installs a subset. A missing name fails the install, and the catalog lists only the selection.

Installed files¶

A checkout install writes:

~/.agents/skills/<skill>        skill links or copies
~/.agents/omics-skills/         router (skill_index.py) and catalog.json
~/.claude/agents/<agent>.md     Claude agent links or copies
~/.claude/skills                link to ~/.agents/skills
~/.codex/agents/<agent>.toml    rendered Codex agents
~/.codex/skills                 link to ~/.agents/skills

An existing directory with a pack skill's name is moved to ~/.agents/omics-skills/previous-skills/. A link with that name is replaced.
An installed agent identical to the new one is left in place. A differing file is kept once as a timestamped .bak file.
If ~/.claude/skills or ~/.codex/skills is a real directory, the installer stops instead of hiding its contents. Merge it into ~/.agents/skills, or install with LINK_CLIENT_SKILLS=no.
Files that do not belong to the pack are not touched.

Install as a plugin¶

Claude Code:

claude plugin marketplace add fmschulz/omics-skills
claude plugin install omics-skills@omics-skills

Codex CLI:

codex plugin marketplace add fmschulz/omics-skills
codex plugin add omics-skills@omics-skills

To test a local checkout, pass . to marketplace add instead of the repository name.

The Claude Code plugin provides the agents and skills; the Codex plugin provides the skills. The router, the catalog, the routing hint hook and the Codex agents come only with a checkout install.

To update, refresh the marketplace and then the plugin. Claude Code: claude plugin marketplace update omics-skills, then claude plugin update omics-skills@omics-skills and a restart. Codex CLI: codex plugin marketplace upgrade omics-skills, then codex plugin add omics-skills@omics-skills again.

Start an agent¶

Claude Code:

claude --agent omics-scientist

Codex CLI: start codex, then ask it to delegate to omics-scientist, or name a skill such as $bio-annotation.

After a checkout install, the router shows which agent and skills fit a task:

python3 ~/.agents/omics-skills/skill_index.py route "annotate these proteins"

Routing hint hook¶

The optional hook runs the router on each prompt and adds a short hint for Claude Code and Codex. When the router fails, the hook exits without blocking the prompt.

make install-hook
make hook-status

Turn it off for one shell with export OMICS_SKILLS_AUTOROUTE=0. Remove it with make uninstall-hook.

Check, update and remove¶

Task	Command
Show what is installed	`make status`
Check that every agent and skill is installed	`make validate`
Update a checkout install	`git pull && make install`
Apply an edited agent prompt to Codex	`make install-codex`
Remove the pack (pack entries only)	`make uninstall`, `make uninstall-claude` or `make uninstall-codex`
Delete agent backups and archived skill directories	`make clean`

Troubleshooting¶

Problem	Fix
Codex does not show an agent change	Run `make install-codex`.
Skills are missing after the checkout moved	Run `make install` from the new location; links keep the old path.
The router does not pick a skill	Run `python3 scripts/skill_index.py route "<task>" --json`, then check the skill description and the agent's `Task Recognition Patterns`.
A local plugin is not listed	Run `codex plugin marketplace list`, `codex plugin list --available --json` and `claude plugin validate .`.