setup-medsci

setup-medsci is a skill for Claude Code from Aperivue/medsci-skills. It costs 59 tokens per session (1,004 once invoked), scanned A, original, MIT.

A read-only checklist that checks whether a medical research computer has the required tools and connections configured.

In plain words
What is it for?
Use it to check Python, R, Node, Claude Code, Git, Zotero, and configured MCP servers before running MedSci Skills.
Why use it?
It shows what is installed, what is missing, and where to find the relevant setup instructions without changing the computer.

Skill for Claude Code

Written for Claude Code: shipped in a Claude Code plugin. Also seen: reads .claude/ paths; mentions Claude Code.

Part of the medsci-presentation plugin — 5 skills shipped together

Good fit Use it to check Python, R, Node, Claude Code, Git, Zotero, and configured MCP servers before running MedSci Skills.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/aperivue/medsci-skills/setup-medsci
Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent
npx skills add Aperivue/medsci-skills --skill setup-medsci
Clone the repo
git clone --depth 1 https://github.com/Aperivue/medsci-skills

Made for: Claude Code.

Or install medsci-presentation, the plugin that ships this one along with the rest of its 5 skills.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for setup-medsci

README.md
[![agentmods](https://agentmods.dev/badge/skills/aperivue/medsci-skills/setup-medsci/github.svg)](https://agentmods.dev/skills/aperivue/medsci-skills/setup-medsci)
Your own site
<a href="https://agentmods.dev/skills/aperivue/medsci-skills/setup-medsci"><img src="https://agentmods.dev/badge/skills/aperivue/medsci-skills/setup-medsci/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

agentmods 80×15 button for setup-medsci

Your own site · 80×15
<a href="https://agentmods.dev/skills/aperivue/medsci-skills/setup-medsci"><img src="https://agentmods.dev/badge/skills/aperivue/medsci-skills/setup-medsci.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 59 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 1,004 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe. Third-party audits
  • NVIDIA SkillSpector warn 7 Sept 2026
SkillSpector: 1 finding, up to medium

These are SkillSpector’s own severities. On a checked sample its high-severity flags on skills were ~96% false positives — a documented command, a public API, a “never do X” rule — so we show them as a caution to read, not a verdict. Why →

  • medium Rogue Agent · line 96
    Skill establishes unauthorized persistence across sessions via cron jobs, startup scripts, or state files. Session persistence allows an attacker to maintain access beyond the current interaction.
    Fix: Remove any persistence mechanisms (cron jobs, startup scripts, state files). Skills should not maintain state across sessions without explicit user consent.
How audits are shown
Origin original No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.00059 $0.01004
Opus 5.5 $0.00024 $0.00402
Sonnet 5.5 $0.00012 $0.00201
Haiku 4.5 $0.00006 $0.00100

Measured 25d ago against content hash 4f30f5b7db56, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

setup-medsci scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 25d ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

skills/setup-medsci/SKILL.md · 86 lines

How it starts

The opening of the file, as written. The whole thing — 86 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Setup-MedSci Skill

Diagnose only. Never install, upgrade or configure anything — no brew install, winget install, pip install, Rscript -e 'install.packages(...)', and no edits to ~/.claude.json or any MCP configuration (read claude mcp list only) — because auto-installers for system Python and R are a support nightmare for non-developer users. If a tool is missing, the user follows the setup doc themselves. Skill versions and content are out of scope (validate_skills.sh, /manage-project status).

The diagnostic table is in English so it can be pasted into a GitHub issue. Remediation links point to the docs/setup/ guides in the medsci-skills repository, and only these five exist: docs/setup/README.md, docs/setup/mac.md, docs/setup/windows.md, docs/setup/mcp-setup.md, docs/setup/common-issues.md.

Workflow

Phase 1: Detect OS

uname -s
  • Darwin → macOS → docs/setup/mac.md
  • Linux → Linux (similar tooling to Mac) → docs/setup/mac.md
  • MINGW*, MSYS*, CYGWIN*, or detection failure on Windows → docs/setup/windows.md

Phase 2: Run Diagnostic Commands

Read references/setup-checklist.md and run every check in it — R1-R5 required, O1-O5 optional — with its detect command, version command, minimum version and status rule. Use command -v <tool> first to detect presence without running it (avoids triggering long initialization). Capture the version output and the exit code, and report the version exactly as printed: if a command fails, report the failure verbatim rather than a version that is "probably" installed. If command -v finds the tool but the version command or its parse fails, mark the row ❌ and report the failing command — the install is broken, not just outdated. An MCP server is ✅ only when claude mcp list shows it connected; configured-but-disconnected is ⚠️.

Phase 3: Emit Checklist Table

Print a single Markdown table to stdout in this exact format, one row per check, with the doc link from the reference for the detected OS:

Read the full file on GitHub · 86 lines

Files

What ships with it

2 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 25d ago Changed · -25 lines · -3 tokens per session 4f30f5b7db56
  2. 1mo ago First seen · 111 lines · 62 tokens per session scan A d346a9b883f6

Subscribe to this mod's changes

setup-medsci is a skill published in the GitHub repository Aperivue/medsci-skills (349 stars, last pushed yesterday), licensed MIT. It adds 59 tokens to every session and 1,004 once invoked, about $0.0002 per session on Opus 5.5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

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