cx-alphagenome-variant-analysis

name	cx-alphagenome-variant-analysis
description	Analyze how a single non-coding genetic variant affects gene expression, chromatin accessibility, histone marks, transcription factors, and splicing using the AlphaGenome API. Use when the user gives a variant in chr:pos:ref/alt form and asks about regulatory or splicing effects, tissue-specific impact, or pathogenicity of a non-coding change. Requires an AlphaGenome API key.

Cx Alphagenome Variant Analysis

Use this Codex adapter for the pinned upstream scientific skill.

Catalog status

• Status: inactive
• Source: cx
• Audit reasons: credentials-required
• Upstream license: Apache-2.0
• Inventory: ../../inventory.json
• Upstream instructions: ../../../authored-skills/alphagenome-variant-analysis/SKILL.md

Procedure

1. Resolve the plugin root as three directories above this skill directory.
2. Read the matching inventory record and verify its status, reasons, source path, and pinned revision.
3. Do not read the upstream instructions until the user has seen every audit reason and given explicit acknowledgement. Acknowledgement permits instruction inspection only.
4. Treat upstream frontmatter as source metadata, not as Codex configuration. Follow the instruction body only where it is compatible with available Codex tools and the current user-approved plan.
5. Treat tools named for another agent runtime as capability requests. Map them to an available Codex tool only when the behavior is equivalent; otherwise report the unavailable capability.
6. Ask before credentials, package installation, new network hosts, remote compute, writes, paid services, destructive actions, or imported executable code.
7. Use $science-provenance for produced scientific outputs and $science-review before presenting scientific claims.

Boundaries

• This wrapper does not grant credentials, network access, package installation, or script execution.
• Do not change an inactive record to active from inside a research task.
• Preserve failures, uncertainty, source identifiers, and licensing constraints.