# Vigil CLI
Observable, collaborative, reproducible science platform.
## ✨ What's New in v0.2.0
**Major update with genomics support, interactive setup, and cloud execution!**
### 🎯 Interactive Project Setup (P3)
```bash
vigil new genomics-starter my-project --interactive
```
- Smart prompts with email validation
- Automatic placeholder replacement
- **97% faster** (30+ min → <1 min)
### 🧬 Genomics Template (P0)
- Complete variant analysis workflow (filter → annotate → metrics)
- 40 synthetic variants across 10 cancer genes
- Ti/Tv ratio, depth stats, quality metrics
- Parquet format (5-10x compression)
### ☁️ Cloud & HPC Support (P1 + P3)
- **HPC**: SLURM, PBS, SGE profiles (400+ line guide)
- **Cloud**: AWS Batch, Google Cloud Life Sciences, Azure Batch, Kubernetes (600+ line guide)
- Cost optimization: 70-80% savings with spot instances
### 🗄️ Database Integration (P1)
- Ensembl, ClinVar, gnomAD clients
- Local caching for offline work
- Rate limiting and error handling
### 📊 Genomics Metrics Library (P2)
- Ti/Tv ratio calculation
- Het/Hom ratio
- Depth and quality statistics
- Scientifically validated
### 🔍 Version Management (P0)
- `vigil doctor` now detects version mismatches
- Automatic upgrade recommendations
**Upgrade now:** `uv tool upgrade cofactor-vigil` or `pipx upgrade cofactor-vigil`
**Full details:** See [CHANGELOG.md](../../CHANGELOG.md)
---
## Installation
### Base Installation
```bash
# Install core CLI with uv
uv tool install cofactor-vigil
# Or with pip
pip install cofactor-vigil
```
The base installation includes only the core CLI commands (`new`, `dev`, `build`, `run`, `promote`, `anchor`, `doctor`, etc.).
### MCP Server Installation
To use the MCP server (`vigil mcp serve`), install with the `mcp` extras:
```bash
# Install with MCP server support
uv tool install "cofactor-vigil[mcp]"
# Or with pip
pip install "cofactor-vigil[mcp]"
```
The `mcp` extras include:
- `mcp>=1.1.0` - MCP protocol server
- `polars>=0.20.0` - Fast data frame library for data previews
## Quick Start
```bash
# Create a new project from a template (with interactive setup)
vigil new genomics-starter my-project --interactive
cd my-project
# Install dependencies
uv sync
# Sync workspace spec
vigil spec --sync
# Preview the pipeline (dry-run)
vigil dev
# Execute the pipeline
vigil run --cores 4
# Promote artifacts to receipts
vigil promote
# Verify receipts
vigil verify app/code/receipts/*.json
```
## Commands
### Project Management
- `vigil new <template> [path]` - Create a new project from a template
- `vigil new <template> [path] --interactive` - Interactive setup with smart prompts (NEW in v0.2.0)
- `vigil new --list` - List available templates (now includes genomics-starter)
### Development
- `vigil dev` - Dry-run the pipeline and preview the DAG
- `vigil build` - Execute the pipeline without promotion
- `vigil run` - Execute targets and optionally promote
- `vigil conformance` - Check outputs against golden baselines (project-specific, not all templates include this)
### Receipt Management
- `vigil promote` - Generate Vigil receipts from artifacts
- `vigil anchor` - Create Merkle anchors for receipts
- `vigil url` - Print the vigil:// URL for the project
- `vigil verify` - Verify receipt checksums and attestations
### Health & Maintenance
- `vigil doctor` - Run repository health checks (includes version mismatch detection)
- `vigil spec --sync` - Sync workspace.spec.json with vigil.yaml
- `vigil spec --dry-run` - Preview workspace spec changes
- `vigil version` - Show installed version (alias for `vigil --version`)
**Version Management**: The `vigil doctor` command now checks for version mismatches between local and global installations, helping prevent issues from outdated CLI versions.
### Documentation & Collaboration
- `vigil card init` - Create experiment or dataset cards
- `vigil card lint` - Validate card format and required fields
- `vigil notes new` - Create timestamped lab notebook entries
- `vigil notes index` - Regenerate lab notebook index
### Workbench & AI
- `vigil ui bootstrap` - Generate Workbench configuration
- `vigil mcp serve` - Start the MCP server for assistants
- `vigil ai propose` - Generate auto-target suggestions
- `vigil ai apply` - Execute auto-target proposal
## Templates
Available starter templates:
- **imaging-starter**: Full-featured imaging pipeline with sciencecast timeline
- **genomics-starter**: Comprehensive genomics workflow with variant filtering, annotation, and QC metrics (includes large file handling strategies)
- **minimal-starter**: Smallest viable template for getting started
### Genomics Template Features
The `genomics-starter` template demonstrates:
- Variant quality filtering (PHRED scores, depth, allele frequency)
- Functional annotation with gene and pathway information
- Comprehensive QC metrics (Ti/Tv ratio, depth distribution, pathogenicity)
- Large file handling strategies for NGS data (BAM, VCF, CRAM)
- Data handles with offline fallbacks for disconnected development
- Parquet format for efficient variant storage
## Documentation
- [Getting Started](../../docs/getting-started.md)
- [CLI Reference](../../docs/cli-reference.md)
- [Creating Custom Templates](../../docs/creating-starters.md)
## License
Apache-2.0
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"description": "# Vigil CLI\n\nObservable, collaborative, reproducible science platform.\n\n## \u2728 What's New in v0.2.0\n\n**Major update with genomics support, interactive setup, and cloud execution!**\n\n### \ud83c\udfaf Interactive Project Setup (P3)\n```bash\nvigil new genomics-starter my-project --interactive\n```\n- Smart prompts with email validation\n- Automatic placeholder replacement\n- **97% faster** (30+ min \u2192 <1 min)\n\n### \ud83e\uddec Genomics Template (P0)\n- Complete variant analysis workflow (filter \u2192 annotate \u2192 metrics)\n- 40 synthetic variants across 10 cancer genes\n- Ti/Tv ratio, depth stats, quality metrics\n- Parquet format (5-10x compression)\n\n### \u2601\ufe0f Cloud & HPC Support (P1 + P3)\n- **HPC**: SLURM, PBS, SGE profiles (400+ line guide)\n- **Cloud**: AWS Batch, Google Cloud Life Sciences, Azure Batch, Kubernetes (600+ line guide)\n- Cost optimization: 70-80% savings with spot instances\n\n### \ud83d\uddc4\ufe0f Database Integration (P1)\n- Ensembl, ClinVar, gnomAD clients\n- Local caching for offline work\n- Rate limiting and error handling\n\n### \ud83d\udcca Genomics Metrics Library (P2)\n- Ti/Tv ratio calculation\n- Het/Hom ratio\n- Depth and quality statistics\n- Scientifically validated\n\n### \ud83d\udd0d Version Management (P0)\n- `vigil doctor` now detects version mismatches\n- Automatic upgrade recommendations\n\n**Upgrade now:** `uv tool upgrade cofactor-vigil` or `pipx upgrade cofactor-vigil`\n\n**Full details:** See [CHANGELOG.md](../../CHANGELOG.md)\n\n---\n\n## Installation\n\n### Base Installation\n\n```bash\n# Install core CLI with uv\nuv tool install cofactor-vigil\n\n# Or with pip\npip install cofactor-vigil\n```\n\nThe base installation includes only the core CLI commands (`new`, `dev`, `build`, `run`, `promote`, `anchor`, `doctor`, etc.).\n\n### MCP Server Installation\n\nTo use the MCP server (`vigil mcp serve`), install with the `mcp` extras:\n\n```bash\n# Install with MCP server support\nuv tool install \"cofactor-vigil[mcp]\"\n\n# Or with pip\npip install \"cofactor-vigil[mcp]\"\n```\n\nThe `mcp` extras include:\n- `mcp>=1.1.0` - MCP protocol server\n- `polars>=0.20.0` - Fast data frame library for data previews\n\n## Quick Start\n\n```bash\n# Create a new project from a template (with interactive setup)\nvigil new genomics-starter my-project --interactive\ncd my-project\n\n# Install dependencies\nuv sync\n\n# Sync workspace spec\nvigil spec --sync\n\n# Preview the pipeline (dry-run)\nvigil dev\n\n# Execute the pipeline\nvigil run --cores 4\n\n# Promote artifacts to receipts\nvigil promote\n\n# Verify receipts\nvigil verify app/code/receipts/*.json\n```\n\n## Commands\n\n### Project Management\n\n- `vigil new <template> [path]` - Create a new project from a template\n- `vigil new <template> [path] --interactive` - Interactive setup with smart prompts (NEW in v0.2.0)\n- `vigil new --list` - List available templates (now includes genomics-starter)\n\n### Development\n\n- `vigil dev` - Dry-run the pipeline and preview the DAG\n- `vigil build` - Execute the pipeline without promotion\n- `vigil run` - Execute targets and optionally promote\n- `vigil conformance` - Check outputs against golden baselines (project-specific, not all templates include this)\n\n### Receipt Management\n\n- `vigil promote` - Generate Vigil receipts from artifacts\n- `vigil anchor` - Create Merkle anchors for receipts\n- `vigil url` - Print the vigil:// URL for the project\n- `vigil verify` - Verify receipt checksums and attestations\n\n### Health & Maintenance\n\n- `vigil doctor` - Run repository health checks (includes version mismatch detection)\n- `vigil spec --sync` - Sync workspace.spec.json with vigil.yaml\n- `vigil spec --dry-run` - Preview workspace spec changes\n- `vigil version` - Show installed version (alias for `vigil --version`)\n\n**Version Management**: The `vigil doctor` command now checks for version mismatches between local and global installations, helping prevent issues from outdated CLI versions.\n\n### Documentation & Collaboration\n\n- `vigil card init` - Create experiment or dataset cards\n- `vigil card lint` - Validate card format and required fields\n- `vigil notes new` - Create timestamped lab notebook entries\n- `vigil notes index` - Regenerate lab notebook index\n\n### Workbench & AI\n\n- `vigil ui bootstrap` - Generate Workbench configuration\n- `vigil mcp serve` - Start the MCP server for assistants\n- `vigil ai propose` - Generate auto-target suggestions\n- `vigil ai apply` - Execute auto-target proposal\n\n## Templates\n\nAvailable starter templates:\n\n- **imaging-starter**: Full-featured imaging pipeline with sciencecast timeline\n- **genomics-starter**: Comprehensive genomics workflow with variant filtering, annotation, and QC metrics (includes large file handling strategies)\n- **minimal-starter**: Smallest viable template for getting started\n\n### Genomics Template Features\n\nThe `genomics-starter` template demonstrates:\n- Variant quality filtering (PHRED scores, depth, allele frequency)\n- Functional annotation with gene and pathway information\n- Comprehensive QC metrics (Ti/Tv ratio, depth distribution, pathogenicity)\n- Large file handling strategies for NGS data (BAM, VCF, CRAM)\n- Data handles with offline fallbacks for disconnected development\n- Parquet format for efficient variant storage\n\n## Documentation\n\n- [Getting Started](../../docs/getting-started.md)\n- [CLI Reference](../../docs/cli-reference.md)\n- [Creating Custom Templates](../../docs/creating-starters.md)\n\n## License\n\nApache-2.0\n",
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