Phase 4 of building a Claude Managed Agent — make it run without you. Turn a graded agent into a recurring scheduled deployment (POSIX-cron), an event-driven curl trigger, or confirmed on-demand use, then finalize the versioned roadmap. Use when the user says "run it every morning", "put it on a schedule", "nightly", "weekly", "automate this", "make it recurring", or when the orchestrator routes phase=run-without-you. deployment_builder.py builds the POST /v1/deployments payload (initial_events must include user.message; optionally nests a user.define_outcome so each firing self-grades); cron_validator.py validates the 5-field cron + IANA timezone and prints the wall-clock DST note; next_directions_writer.py writes NEXT-DIRECTIONS.md. No tool makes API calls — the deployment is created via BYOK curl. Distinct from grade-iterate (the in-session loop) and wrap-up (closeout).

Statistical analysis and reporting for experimental datasets; use when you need to interpret experimental results, test significance (t-tests/ANOVA), or generate reproducible reports.

Phase 1 of building a Claude Managed Agent — interview the founder about the one job the agent should do, then produce a build sheet (CMA primitives table + v1/v2 deferrals + eval plan) WITHOUT needing their API key yet. Use when the user says "help me scope an agent", "I have an idea for an agent", "what should this agent be", or when the orchestrator routes phase=interview. Drives the six intake slots (job, trigger, inputs, actions, definition-of-done, recurrence) via AskUserQuestion, maps them to primitives with interview_planner.py, assembles build-sheet.json with build_sheet_builder.py, and validates limits with primitives_validator.py. Connectors are mockable in v0 (schema-true custom tools); real MCP servers become v1 deferrals. Distinct from stage-launch (which turns the sheet into payloads).

Phase 3 of building a Claude Managed Agent — the bounded grade→iterate loop. Define a CMA outcome (a required markdown rubric graded by an isolated grader), read each verdict, decide the next move (sharpen / re-run / promote to schedule), and once a version passes, run held-back eval cases in parallel. Use when the user says "grade my agent", "make it pass the rubric", "iterate until it's good", "is it good enough", or when the orchestrator routes phase=grade-iterate. outcome_builder.py builds the user.define_outcome payload (rubric required, max_iterations clamped 1..20 — never unbounded); verdict_reader.py reads the grader result and recommends the next move; eval_scaffold.py generates held-back cases + a parallel run plan (capped at the 25-thread CMA ceiling). Distinct from stage-launch (first launch) and run-without-you (scheduling).

ETE (Environment for Tree Exploration) toolkit for phylogenetic and hierarchical tree analysis; use it when you need to parse/manipulate Newick/NHX trees, detect duplication/speciation events, integrate NCBI taxonomy, and render publication-quality figures.

Performs epidemiological analyses including disease modeling (SIR/SEIR), outbreak investigation, risk factor identification, incidence/prevalence estimation, and causal inference from observational data; trigger when users discuss disease spread, public health data, or populat...

Use when a user wants to build, launch, grade, or schedule a Claude Managed Agent (CMA) in their own Anthropic account — "build me an agent", "launch this as a managed agent", "run this on a schedule", "grade my agent against a rubric", "set up a nightly worker". Reads the per-session goal (./my-agent/goal.json), routes deterministically to one of five phase sub-skills (interview → stage-launch → grade-iterate → run-without-you → wrap-up) via goal_router.py, and compiles the goal+phase into an execution shape (single-pass workflow / bounded grade→iterate loop / recurring cron deployment loop) via loop_compiler.py. Forks context so heavy intake (build sheets, payloads, eval cases) stays out of the parent thread. All launches are emitted as BYOK curl the user runs with their own key; no tool makes API calls. Inspired by anthropics/launch-your-agent (Apache-2.0). Distinct from engineering/agent-harness (generic domain loop) and engineering/write-a-skill (authors Claude Code skills, not CMAs).

Runs a disciplined Discuss -> Map -> Decompose -> Execute -> Verify loop that grounds code in verified structure — no invented APIs, no assumed imports, no placeholder code — with a lazy-senior-dev YAGNI ladder that deletes unnecessary code before it is written. Use when a coding task is high-stakes, complex, or spans existing code (auth, databases, migrations, multi-file features), or when the user explicitly asks to plan carefully before coding, avoid hallucinated code, or work rigorously. Not for trivial edits, typos, or throwaway one-off scripts — those do not need the full loop.

Use when the user needs YouTube transcripts, video search, channel browsing, playlist extraction, or content monitoring. Trigger phrases: 'get the transcript for', 'search YouTube for', 'what are the latest videos on', 'list this playlist', 'monitor this channel', or any request involving a YouTube URL, video ID, or @handle. Do NOT use for downloading video or audio files, YouTube engagement data (likes, comments), or private/age-restricted videos.

DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, process FASTQ/BAM/VCF, for developing and executing genomics pipelines.

X/Twitter growth engine for building audience, crafting viral content, and analyzing engagement. Use when the user wants to grow on X/Twitter, write tweets or threads, analyze their X profile, research competitors on X, plan a posting strategy, or optimize engagement. Complements social-content (generic multi-platform) with X-specific depth: algorithm mechanics, thread engineering, reply strategy, profile optimization, and competitive intelligence via web search.

Analyzes clinical diagnostic accuracy studies for bias using the QUADAS-2 tool. Use when Claude needs to assess the quality, risk of bias, or applicability of diagnostic accuracy studies (e.g., "Assess this paper using QUADAS-2").

Create new agent skills with proper structure, progressive disclosure, and bundled resources. Use when user wants to create, write, build, or author a new skill.

Close out a launched Claude Managed Agent — recap every primitive the founder now owns, regenerate the single-file overview page, and suggest the next 1-2 upgrades. Use when the user says "wrap up", "close this out", "what do I own now", "give me the summary", "recap the agent", or when the orchestrator routes phase=wrap-up. primitives_inventory.py tables everything owned (agent, environment, session, memory, outcome, deployment); overview_page.py regenerates a self-contained ./my-agent/agent-overview.html; upgrade_suggester.py ranks the next moves from recorded deferrals plus standing hardening steps. Companion to run-without-you; the last stop before phase=done.

Design and write deterministic multi-agent workflow scripts (.js files in .claude/workflows/) for Claude Code's Workflow tool. Use when a user wants to build, create, author, scaffold, or run a custom Claude Code workflow, orchestrate sub-agents (fan-out, pipeline, loop, judge-panel), or automate a repeatable multi-step task across fresh-context agents.

NGS analysis toolkit. Used for BAM to bigWig conversion, quality control (correlation, PCA, fingerprint plots), heatmaps/feature plots (TSS, peaks), suitable for ChIP-seq, RNA-seq, ATAC-seq visualization.

Query the LLM Wiki — reads index.md first, drills into 3-10 relevant pages, synthesizes an answer with inline [[wikilink]] citations, and offers to file the answer back as a new comparison or synthesis page. Usage /wiki-query "<question>"

Transform, clean, reshape, and preprocess data using pandas and numpy. Works with ANY LLM provider (GPT, Gemini, Claude, etc.).

Show recent entries from the LLM Wiki log (wiki/log.md). Uses the standardized

Run a health check on the LLM Wiki vault — mechanical checks (orphans, broken links, stale pages, missing frontmatter, log gap, duplicates) plus semantic checks (contradictions, cross-reference gaps, concepts missing their own page). Outputs a markdown report with suggested actions. Usage /wiki-lint [--stale-days N] [--log-gap-days N]