lyra

Agentic primitives repository. Provides reusable agents, instructions, prompts, and skills for AI-assisted development workflows, managed via the Microsoft Agentic Package Manager (APM).

Contents

The .apm/ directory contains the following primitive types:

Type	Description
agents/	Custom GitHub Copilot agents for orchestrating development workflows
instructions/	Coding guidelines applied automatically to matching file types
prompts/	Reusable prompt templates
skills/	Reusable skill definitions

Setup

Requires Python 3.13+ and uv.

just dev

This creates a virtual environment, installs all dependencies, and drops you into an activated shell.

Using as an APM Dependency

Quick Install

Install a conductor agent and all its dependencies:

# For Nextflow projects
apm install FrancisCrickInstitute/lyra/agents/nextflow/conductor.agent.md

# For Python projects
apm install FrancisCrickInstitute/lyra/agents/python/python-conductor.agent.md

Or install a curated bundle as a single dependency path:

# Nextflow bundle (conductor + subagents/skills)
apm install FrancisCrickInstitute/lyra/packages/nextflow
apm install

# Python bundle (conductor + subagents)
apm install FrancisCrickInstitute/lyra/packages/python
apm install

Project Configuration

Or declare in your project's apm.yml:

name: my-project
version: 0.0.0
dependencies:
  apm:
    - FrancisCrickInstitute/lyra/agents/nextflow/conductor.agent.md
    - FrancisCrickInstitute/lyra/agents/nextflow/nextflow-subagents/code-review-subagent.agent.md
    - FrancisCrickInstitute/lyra/agents/nextflow/nextflow-subagents/planning-subagent.agent.md

Then run:

apm install

Notes on Paths

• APM supports installing owner/repo/path packages (subdirectory/virtual packages).
• APM does not support wildcard folder installs (for example, "install all files under this folder" via glob).
• If you need a fixed set of primitives from this repo, prefer bundle paths like FrancisCrickInstitute/lyra/packages/nextflow or FrancisCrickInstitute/lyra/packages/python.

Install Individual Components

You can also install specific components:

# Just a skill
apm install FrancisCrickInstitute/lyra/skills/nextflow-diagram-creation

# Specific subagent
apm install FrancisCrickInstitute/lyra/agents/nextflow/nextflow-subagents/planning-subagent.agent.md
apm install FrancisCrickInstitute/lyra/agents/python/python-subagents/python-planner-subagent.agent.md

Troubleshooting: "not accessible or doesn't exist"

APM uses the GitHub API, which rate-limits unauthenticated requests to 60/hour. If you hit this limit, installs will fail with "not accessible or doesn't exist" even though the file is public.

Fix: set GITHUB_APM_PAT using your existing gh CLI token:

export GITHUB_APM_PAT=$(gh auth token)

To make this permanent, add it to your shell profile (~/.zshrc or ~/.bashrc):

echo 'export GITHUB_APM_PAT=$(gh auth token)' >> ~/.zshrc

This raises the rate limit to 5,000 requests/hour.