ワンクリックでManusで任意のスキルを実行

setup

スター19

フォーク11

更新日2026年7月19日 04:39

Use when the user invokes `/setup` (or asks to "configure setup", "run setup wizard", "configure the academic-research project/plugin"), asks to configure the academic-research plugin, add or rotate API keys (Zotero, Elsevier, WoS, Semantic Scholar, Wiley TDM, OpenAlex, Gemini), register MCP servers, or patch permission rules. Also fires when another academic-research skill (zotero-operations, systematic-review, fact-check, critic-loop) reports `NOT CONFIGURED` on its pre-flight check.

インストール

Codex または Claude でインストールこの Prompt をコピーして Codex、Claude、または他のアシスタントに貼り付けると、Skill ページを確認してインストールできます。

Manusで実行

ソース

mronkko

mronkko/claude-academic-research

GitHub リポジトリを開く Creator のリポジトリを見る

ダウンロード

Manusで実行

setup

Quick definitions (T4-5; full glossary at skills/_glossary.md):

A plugin is the code bundle this setup is configuring — a downloadable package shipped with skills, pipeline scripts, and templates that the agentic environment uses for academic-research work.

A skill is a prose rule-book the agent loads when your request matches its trigger phrases. Skills tell the agent how to approach a task; they don't run code on their own. setup, zotero- operations, systematic-review, etc. are all skills in this plugin.

An MCP server is a small helper program the agent talks to in the background. Example: the Zotero MCP server lets the agent read and update your Zotero library directly. The wizard checks five MCP servers (Zotero, Scopus, Semantic Scholar, OpenAlex, paper-search) and offers to register the missing ones.

Setup runs as a terminal wizard the user executes. The agent's role is only to give them the command and confirm when they are done. Do not run any tool calls — no Bash, no Read, no probes. All the information needed is already known:

Wizard path: ${CLAUDE_PLUGIN_ROOT}/scripts/setup/wizard.py (or project-relative ./scripts/setup/wizard.py if not running inside Claude Code or Antigravity) — The active plugin version's absolute path (or project-relative fallback if ${CLAUDE_PLUGIN_ROOT} is not defined) is used, so the user has a concrete path to run.
Config written to: ~/.config/academic-research/config.toml (mode 0600).
Settings patched: ~/.claude/settings.json (backed up as .bak-wizard, bypassed silently if not running under Claude).
Antigravity MCP config: if Antigravity (agy) is detected, the same MCP servers are also registered into ~/.gemini/config/mcp_config.json (backed up as .bak-wizard). Permission rules are not patched for Antigravity — only Claude Code's ~/.claude/settings.json is.
Wizard is idempotent: re-running updates or adds keys without clobbering existing ones.

Procedure

CRITICAL: never ask the user to paste API keys into the chat. Any text typed into the chat is transmitted to the model provider. The wizard exists so keys stay local.

Paste the following message to the user (no tool calls needed — just text):

I'll hand you the setup wizard. It runs in your terminal, prompts for each API key with hidden input (keystrokes don't appear), then checks five MCP (Model Context Protocol) servers and offers to register any that are missing: Zotero (required — every citation skill uses it), at least one of Scopus / Semantic Scholar / OpenAlex (required for literature search to work), and paper-search (optional — for ArXiv / PubMed PDF retrieval). It then writes your config file locally. Your keys never pass through the chat.

Run the setup wizard in your terminal. If the ${CLAUDE_PLUGIN_ROOT} environment variable is defined:
python3 ${CLAUDE_PLUGIN_ROOT}/scripts/setup/wizard.py
Otherwise, run the project-relative command from the root of your workspace:
python3 ./scripts/setup/wizard.py
How to open a terminal if you are not already in one:

macOS: ⌘-Space → type Terminal → Enter.

Windows: Windows key → type PowerShell → Enter. If python3 is not recognised, try python instead.

Linux: Ctrl-Alt-T (or your distro's terminal app).

Already running the agent in a terminal? Either open a new tab and run it there, or temporarily exit this session, run the wizard, and then resume this conversation.

When the wizard prints "Setup complete", return here and say "done" (or similar). I'll confirm and we'll continue.

After the user says they finished the wizard, respond with a short confirmation ("Setup done. Ready for the next task.") and let the next conversational turn drive the work. Do not run a verification Bash call — if something went wrong with the wizard, the user's next invocation of zotero-operations / systematic-review / etc. will hit its own pre-flight check and bounce here again.

If the wizard reports errors

The wizard prints to stdout. If the user pastes output showing a problem:

Python missing: tell them to install Python 3.11+ — macOS can use Homebrew (brew install python), Windows can use python.org's installer (check "Add Python to PATH"), Linux uses the distro's package manager.
Tkinter not required — the wizard is terminal-only. Any Python 3.11+ install works.
Permission denied writing config: user's home directory has unusual permissions. Unlikely on a single-user machine.
Can't parse existing settings.json: the file is malformed. The wizard backs up to .bak-wizard before touching; restore from there, fix manually, or delete and re-run.
MCP register fails with "command not found": the underlying MCP binary is not installed. The wizard prints the project's homepage and the exact install command (uv tool install "zotero-mcp-server[scite,semantic]" — the extras add Scite retraction checks and semantic search; uv tool install scopus-mcp, or "requires Node.js + npm" for the npx-based servers). Install it, then re-run the wizard — it's idempotent and picks up where it left off.
zotero-cli missing or zotero-mcp found but not zotero-cli: installing zotero-mcp-server also puts the standalone zotero-cli on PATH — no separate step. If the wizard's summary shows zotero-mcp present but zotero-cli absent, the stale PyPI package zotero-mcp (0.1.6, pre-dates the CLI) is shadowing it: uv tool uninstall zotero-mcp then reinstall zotero-mcp-server[scite,semantic] as above. zotero-cli is optional — every skill degrades to MCP tools and zotero_io.py without it — so this never blocks setup.
Wizard exits with code 4: Zotero MCP is not connected. No academic-research skill works without it. The wizard's summary lists the install and registration commands; run them and re-run the wizard.

Red flags

You are about to run a Bash tool call in this skill. Don't. This skill has no Bash probes by design — they cause permission prompts for no benefit. The wizard handles everything.
You are about to ask the user to paste a key into the chat. Never. The wizard is the only acceptable path for keys.
You are about to log, echo, or repeat a key the user typed in any form. The wizard hides input for this exact reason; don't accidentally capture it in follow-up questions.

このリポジトリの他の Skills

同じリポジトリ

systematic-review

mronkko/claude-academic-research

Use when running a full systematic literature review (SLR) — PRISMA-style search, screening, coding, and export. Trigger phrases "systematic review", "SLR", "PRISMA", "screen papers", "code papers", "full-text screening". Do NOT use for isolated Zotero enrichment without a screening pipeline — use `zotero-operations`. Targets social sciences; medical-SLR instruments (RoB 2, ROBINS-I, evidence hierarchies, PRISMA-P) are out of scope.

2026-07-1919

zotero-operations

mronkko/claude-academic-research

Use when the user asks to work with a Zotero library — adding abstracts, attaching PDFs, enriching metadata, importing items, deduplicating, fixing BBT (Better BibTeX) citation keys, or writing child notes. Trigger phrases "add abstracts to Zotero", "attach PDFs", "enrich Zotero library", "fix citation keys", "find duplicates in Zotero", "update Zotero items". Do NOT use for a full PRISMA-style systematic review — use `systematic-review` instead.

2026-07-1919

suggesting-reviewers

mronkko/claude-academic-research

Use when an editor needs to identify peer reviewers OR an associate editor (AE) to handle a manuscript from its abstract — matching the paper's topics and methodology to editorial-board members, associate editors, and external experts and excluding ineligible people. Trigger phrases "suggest reviewers", "find reviewers for this paper", "who could review this", "recommend referees", "reviewer candidates", "suggest an AE", "assign an associate editor", "who should handle this paper", "recommend an AE", "select an associate editor". Do NOT use for writing or revising the manuscript — use `academic-research:critic-loop` / `manuscript-revision`. Do NOT use to verify a draft's citations — use `academic-research:fact-check`.

2026-06-1619

critic-loop

mronkko/claude-academic-research

Use when the user asks to revise, polish, or critique an academic manuscript, chapter, thesis, or paper through parallel critic perspectives. Trigger phrases "/critic-loop", "run critic-loop", "revise this manuscript", "run critics on this draft", "run a critical review", "review this chapter". Invoke as `/critic-loop <document-path>`.

2026-06-1319

manuscript-revision

mronkko/claude-academic-research

Use when the user asks to revise, polish, improve, critique, or finalize an existing academic draft — manuscripts, papers, theses, chapters, dissertations. Trigger phrases "revise this draft", "polish this chapter", "finalize this manuscript", "improve this paper", "critique this section", "review this thesis". Do NOT use for first-draft writing or blank-page work — this skill's doctrine applies once a draft exists and is ready for revision.

2026-06-1319

academic-style

mronkko/claude-academic-research

Use when drafting or editing academic prose — topic sentences, paragraph structure, APA-style citations, active voice, tense, hedging conventions, term definitions. Fires eagerly on any .qmd / .Rmd / .md / .tex file in an academic-research project. Do NOT use for the revision workflow — use `manuscript-revision` + `/critic-loop`. Do NOT use for factual or citation accuracy — use `grounded-citations` / `empirical-integrity` / `fact-check`.

2026-05-2619

name

setup

description

setup

Quick definitions (T4-5; full glossary at skills/_glossary.md):

A plugin is the code bundle this setup is configuring — a downloadable package shipped with skills, pipeline scripts, and templates that the agentic environment uses for academic-research work.

A skill is a prose rule-book the agent loads when your request matches its trigger phrases. Skills tell the agent how to approach a task; they don't run code on their own. setup, zotero- operations, systematic-review, etc. are all skills in this plugin.

An MCP server is a small helper program the agent talks to in the background. Example: the Zotero MCP server lets the agent read and update your Zotero library directly. The wizard checks five MCP servers (Zotero, Scopus, Semantic Scholar, OpenAlex, paper-search) and offers to register the missing ones.

Wizard path: ${CLAUDE_PLUGIN_ROOT}/scripts/setup/wizard.py (or project-relative ./scripts/setup/wizard.py if not running inside Claude Code or Antigravity) — The active plugin version's absolute path (or project-relative fallback if ${CLAUDE_PLUGIN_ROOT} is not defined) is used, so the user has a concrete path to run.
Config written to: ~/.config/academic-research/config.toml (mode 0600).
Settings patched: ~/.claude/settings.json (backed up as .bak-wizard, bypassed silently if not running under Claude).
Antigravity MCP config: if Antigravity (agy) is detected, the same MCP servers are also registered into ~/.gemini/config/mcp_config.json (backed up as .bak-wizard). Permission rules are not patched for Antigravity — only Claude Code's ~/.claude/settings.json is.
Wizard is idempotent: re-running updates or adds keys without clobbering existing ones.

Procedure

CRITICAL: never ask the user to paste API keys into the chat. Any text typed into the chat is transmitted to the model provider. The wizard exists so keys stay local.

Paste the following message to the user (no tool calls needed — just text):

I'll hand you the setup wizard. It runs in your terminal, prompts for each API key with hidden input (keystrokes don't appear), then checks five MCP (Model Context Protocol) servers and offers to register any that are missing: Zotero (required — every citation skill uses it), at least one of Scopus / Semantic Scholar / OpenAlex (required for literature search to work), and paper-search (optional — for ArXiv / PubMed PDF retrieval). It then writes your config file locally. Your keys never pass through the chat.

Run the setup wizard in your terminal. If the ${CLAUDE_PLUGIN_ROOT} environment variable is defined:
python3 ${CLAUDE_PLUGIN_ROOT}/scripts/setup/wizard.py
Otherwise, run the project-relative command from the root of your workspace:
python3 ./scripts/setup/wizard.py
How to open a terminal if you are not already in one:

macOS: ⌘-Space → type Terminal → Enter.

Windows: Windows key → type PowerShell → Enter. If python3 is not recognised, try python instead.

Linux: Ctrl-Alt-T (or your distro's terminal app).

Already running the agent in a terminal? Either open a new tab and run it there, or temporarily exit this session, run the wizard, and then resume this conversation.

When the wizard prints "Setup complete", return here and say "done" (or similar). I'll confirm and we'll continue.

If the wizard reports errors

The wizard prints to stdout. If the user pastes output showing a problem:

Python missing: tell them to install Python 3.11+ — macOS can use Homebrew (brew install python), Windows can use python.org's installer (check "Add Python to PATH"), Linux uses the distro's package manager.
Tkinter not required — the wizard is terminal-only. Any Python 3.11+ install works.
Permission denied writing config: user's home directory has unusual permissions. Unlikely on a single-user machine.
Can't parse existing settings.json: the file is malformed. The wizard backs up to .bak-wizard before touching; restore from there, fix manually, or delete and re-run.
MCP register fails with "command not found": the underlying MCP binary is not installed. The wizard prints the project's homepage and the exact install command (uv tool install "zotero-mcp-server[scite,semantic]" — the extras add Scite retraction checks and semantic search; uv tool install scopus-mcp, or "requires Node.js + npm" for the npx-based servers). Install it, then re-run the wizard — it's idempotent and picks up where it left off.
zotero-cli missing or zotero-mcp found but not zotero-cli: installing zotero-mcp-server also puts the standalone zotero-cli on PATH — no separate step. If the wizard's summary shows zotero-mcp present but zotero-cli absent, the stale PyPI package zotero-mcp (0.1.6, pre-dates the CLI) is shadowing it: uv tool uninstall zotero-mcp then reinstall zotero-mcp-server[scite,semantic] as above. zotero-cli is optional — every skill degrades to MCP tools and zotero_io.py without it — so this never blocks setup.
Wizard exits with code 4: Zotero MCP is not connected. No academic-research skill works without it. The wizard's summary lists the install and registration commands; run them and re-run the wizard.

Red flags

You are about to run a Bash tool call in this skill. Don't. This skill has no Bash probes by design — they cause permission prompts for no benefit. The wizard handles everything.
You are about to ask the user to paste a key into the chat. Never. The wizard is the only acceptable path for keys.
You are about to log, echo, or repeat a key the user typed in any form. The wizard hides input for this exact reason; don't accidentally capture it in follow-up questions.