Bio Single Cell Hashing Demultiplexing
GPTomics/bioSkills
Assign cells to their sample of origin from cell or nucleus hashing (CITE-seq HTOs, MULTI-seq lipid/cholesterol tags, CellPlex CMOs) and call cross-sample doublets using Seurat…
A skill your agent uses when 需要用一个 setup 入口完成 Nucleus 目标仓库初始化引导和宿主工具检查规划。
MITAuto-check passed
Install Setup
$ npx skills add protect-my-hair/nucleus-marketplace --skill setup -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install protect-my-hair/nucleus-marketplace setup --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/protect-my-hair/nucleus-marketplace.git skills-src && mkdir -p .claude/skills && cp -r skills-src/plugins/nucleus/skills/setup .claude/skills/setup && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "setup" agent skill from https://github.com/protect-my-hair/nucleus-marketplace/tree/main/plugins/nucleus/skills/setup into .claude/skills/setup/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "setup", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/protect-my-hair/nucleus-marketplace/tree/main/plugins/nucleus/skills/setupType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add protect-my-hair/nucleus-marketplace --skill setup -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install protect-my-hair/nucleus-marketplace setup --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/protect-my-hair/nucleus-marketplace.git skills-src && mkdir -p .agents/skills && cp -r skills-src/plugins/nucleus/skills/setup .agents/skills/setup && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "setup" agent skill from https://github.com/protect-my-hair/nucleus-marketplace/tree/main/plugins/nucleus/skills/setup into .agents/skills/setup/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "setup", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add protect-my-hair/nucleus-marketplace --skill setup -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install protect-my-hair/nucleus-marketplace setup --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/protect-my-hair/nucleus-marketplace.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/plugins/nucleus/skills/setup .cursor/skills/setup && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "setup" agent skill from https://github.com/protect-my-hair/nucleus-marketplace/tree/main/plugins/nucleus/skills/setup into .cursor/skills/setup/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "setup", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/protect-my-hair/nucleus-marketplace.git --path plugins/nucleus/skills/setup--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add protect-my-hair/nucleus-marketplace --skill setup -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install protect-my-hair/nucleus-marketplace setup --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/protect-my-hair/nucleus-marketplace.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/plugins/nucleus/skills/setup .gemini/skills/setup && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "setup" agent skill from https://github.com/protect-my-hair/nucleus-marketplace/tree/main/plugins/nucleus/skills/setup into .gemini/skills/setup/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "setup", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install protect-my-hair/nucleus-marketplace setupInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add protect-my-hair/nucleus-marketplace --skill setup -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/protect-my-hair/nucleus-marketplace.git skills-src && mkdir -p .github/skills && cp -r skills-src/plugins/nucleus/skills/setup .github/skills/setup && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "setup" agent skill from https://github.com/protect-my-hair/nucleus-marketplace/tree/main/plugins/nucleus/skills/setup into .github/skills/setup/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "setup", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add protect-my-hair/nucleus-marketplace --skill setup -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install protect-my-hair/nucleus-marketplace setup --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/protect-my-hair/nucleus-marketplace.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/plugins/nucleus/skills/setup .opencode/skills/setup && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "setup" agent skill from https://github.com/protect-my-hair/nucleus-marketplace/tree/main/plugins/nucleus/skills/setup into .opencode/skills/setup/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "setup", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
Facts
- Skill name
setup- GitHub stars
- 164
- Token cost
- ~1k tokens
- SKILL.md length
- 254 words
- Files
- 7 (incl. scripts, references, assets)
- Skills in repo
- 18
- Repo updated
- First seen
- Licence
- MIT
At a glance
A skill your agent uses when 需要用一个 setup 入口完成 Nucleus 目标仓库初始化引导和宿主工具检查规划。
- Works in 8 steps: 执行… → 执行 plan：生成统一 setup plan，说明 target… → 执行 approval --auto-defaults：由 setup… → …
- 需要用一个 setup 入口完成 Nucleus 目标仓库初始化引导和宿主工具检查规划
- SKILL.md covers 使用原则, Checklist, 子命令 and 边界, plus 2 more sections
- Runs Python scripts from its folder; calls python3
What it does
Setup is an agent skill from protect-my-hair/nucleus-marketplace. Use when 需要用一个 setup 入口完成 Nucleus 目标仓库初始化引导和宿主工具检查规划。
Its SKILL.md is about 1k tokens, which your agent loads only when the skill is triggered. The skill folder holds 10 other files, including scripts, reference files and assets (for example `agents/openai.yaml`, `assets/setup-summary-template.md` and `references/human-result.md`).
The repository describes itself as: Nucleus — Claude Code / Codex 工作流插件，确保 AI 编码产出结构可信、边界可审计、过程可追溯. The licence is MIT.
When your agent uses it
- 需要用一个 setup 入口完成 Nucleus 目标仓库初始化引导和宿主工具检查规划
Example prompts
- “/setup”
Requirements
- Python 3
Workflow steps
8 steps, taken from the first numbered list in SKILL.md.
- 执行 inspect：同时执行目标仓库只读检查（preflight）和宿主工具只读检查（inspect）。
- 执行 plan：生成统一 setup plan，说明 target scopes、host scopes、默认动作和风险。
- 执行 approval --auto-defaults：由 setup 入口生成本轮默认确认事实；遇到冲突、路径风险或用户级配置风险时停住确认。
- 执行 apply：默认写入 AGENTS.md 受控规则区块、初始化 .ac 工作目录，并为缺失宿主工具生成安装和验证引导。
- 处理 apply 阻塞或安装引导：冲突、越界或用户级配置风险必须停住；宿主工具缺失时按 _shared/references/subagent-precheck-protocol.md 完成 subagentPreReview 并确认材料可提交人工审查，再进入安装确认。
- 执行 verify：统一验证目标仓库初始化状态和宿主工具真实状态。
- 执行 build-result：生成 .nucleus/runs//setup-entry/result.json 和 summary.md。
- 复核宿主工具状态：如果宿主工具仍缺失或未验证，读取安装会话 reference，按 _shared/references/subagent-precheck-protocol.md 完成 subagentPreReview 并确认材料可提交人工审查，再发起安装确认、执行安装…
What it can do on your machine
Read from SKILL.md and the folder at commit 3c82085. It shows what the files ask for, not the result of running them.
Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
Ships 1 file in scripts/ (Python), which the agent can run.
Shell commands in SKILL.md call:
python3
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md.
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Context cost
Setup loads about 1k tokens when it runs, and up to ~2.3k if it reads all its reference files. Until then it costs about 15 tokens; SKILL.md has 254 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
Safety
Auto-check passed
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); the scripts in this folder are not scanned.
SKILL.md
The full file from protect-my-hair/nucleus-marketplace at commit 3c82085, republished under its MIT licence (© protect-my-hair). 254 words, ~1,037 tokens.
Download SKILL.mdSave it as
.claude/skills/setup/SKILL.md (or your agent's skills folder). This skill also uses 6 other files; get the full folder from GitHub.- name
- setup
- description
- Use when 需要用一个 setup 入口完成 Nucleus 目标仓库初始化引导和宿主工具检查规划。
Setup
前置：使用本 Skill 前，先按
using-nucleus完成 Nucleus 入口识别（Claude Code 会话由插件 SessionStart hook 自动注入该纪律）。
setup 是用户主入口。它对人呈现一次 setup 体验，内部仍然编排 target-repo-setup 和 host-tool-setup，不合并两者职责边界。
使用原则
- 用户主要使用本 Skill；
target-repo-setup和host-tool-setup保留为内部能力或高级入口。 target-repo-setup只初始化目标仓库资产，不检查、不安装、不配置宿主工具。host-tool-setup只处理宿主工具检查、规划、确认、验证和回滚证据，不写目标业务产物。- 计划已生成不代表安装成功。仓库初始化完成不代表工具可用。
- 用户主动执行 setup 后，仓库初始化默认继续执行；遇到冲突、路径风险或宿主工具写配置风险时才停下来确认。
- 宿主工具真实可用只能由
verify证据证明。 - 总结果必须分别记录目标仓库初始化和宿主工具状态；目标仓库成功不等于宿主工具成功。
- 如果
hostTools.status不是SUCCEEDED，当前 agent 不得结束本轮 setup 回复；必须读取host-tool-setup/references/host-tool-install-session.md和host-tool-setup/references/tool-installation.md，按共享子代理预审协议（_shared/references/subagent-precheck-protocol.md）完成subagentPreReview并确认材料可提交人工审查，再继续发起安装确认和执行。
<HARD-GATE>
未创建宿主 todo/task 跟踪 setup 步骤时，不得运行 `apply`、`verify` 或 `build-result`。未按宿主任务逐项完成 inspect、plan、approval、apply、verify、build-result 和必要的宿主工具安装复验时，不得把 summary.md、result.json 或 setup plan 当作 setup 终态。
内部 target-repo-setup 或 host-tool-setup 到达人工审查点时，必须先按 _shared/references/subagent-precheck-protocol.md 完成 subagentPreReview 预审并取得"材料可提交人工审查"结论；未预审不得请求人工审批或评审通过。
</HARD-GATE>
Checklist
启动本 Skill 后，必须先为以下每一项创建宿主 todo/task，并按顺序执行；Codex 使用计划 / 任务工具，Claude Code 使用 TodoWrite 或等价宿主 todo。每完成、阻塞、等待确认或需要复验一项，都必须逐项更新状态；任何等待确认若涉及人工审查点，仍必须先有 subagentPreReview 且材料可提交人工审查。
- 执行 inspect：同时执行目标仓库只读检查（preflight）和宿主工具只读检查（inspect）。
- 执行 plan：生成统一 setup plan，说明 target scopes、host scopes、默认动作和风险。
- 执行 approval --auto-defaults：由 setup 入口生成本轮默认确认事实；遇到冲突、路径风险或用户级配置风险时停住确认。
- 执行 apply：默认写入 AGENTS.md 受控规则区块、初始化
.ac工作目录，并为缺失宿主工具生成安装和验证引导。 - 处理 apply 阻塞或安装引导：冲突、越界或用户级配置风险必须停住；宿主工具缺失时按
_shared/references/subagent-precheck-protocol.md完成subagentPreReview并确认材料可提交人工审查，再进入安装确认。 - 执行 verify：统一验证目标仓库初始化状态和宿主工具真实状态。
- 执行 build-result：生成
.nucleus/runs/<workflowRunId>/setup-entry/result.json和summary.md。 - 复核宿主工具状态：如果宿主工具仍缺失或未验证，读取安装会话 reference，按
_shared/references/subagent-precheck-protocol.md完成subagentPreReview并确认材料可提交人工审查，再发起安装确认、执行安装 / 配置 / 激活 / 索引，并重新运行 verify 和 build-result。
summary.md、result.json、setup plan 和 guidance-only report 只是证据，不能替代宿主任务、用户确认、真实安装执行或 verify 结果。
子命令
运行 python3 scripts/setup.py list-subcommands 查看完整能力。
inspect/plan/approval/apply/verify/build-result
边界
- 统一入口证据写入
.nucleus/runs/<workflowRunId>/setup-entry/**。 - 目标仓库初始化证据仍写入
.nucleus/runs/<workflowRunId>/setup/**和.nucleus/runs/<workflowRunId>/result.json。 - 宿主工具证据仍写入
.nucleus/runs/<workflowRunId>/host-tool-setup/**。 - 不得写
docs/requirement/**。不写.autocode/**、.claude/notepads/**、docs/bugfix/**。 - runtime 不写用户级 Codex、Claude Code 或 MCP 配置；真实配置写入只能由当前 agent 按
_shared/references/subagent-precheck-protocol.md完成subagentPreReview并确认材料可提交人工审查后，再向用户确认后执行。 - 不能把宿主工具安装、MCP 配置或激活重新塞回
target-repo-setup。
何时读取资源
- workflow step、artifact、approval 和 result 语义：读
references/workflow-contract.md。 - 人读摘要字段和交付口径：读
references/human-result.md。 - 内部编排边界和禁止事项：读
references/orchestration-boundary.md。 - 宿主工具缺失后的安装确认和执行闭环：读
host-tool-setup/references/host-tool-install-session.md，再读host-tool-setup/references/tool-installation.md，并在subagentPreReview确认材料可提交人工审查后执行。 - 摘要模板来自
assets/setup-summary-template.md。
对人交付口径
inspect / plan / approval / apply 默认静默执行，只在遇到阻塞、冲突或风险时向用户说话。
结束后先读统一 summary.md，再读统一 result.json。回复必须说明仓库初始化做了什么、宿主工具检查到了什么、哪些工具还没有真实可用证据，以及是否因为冲突或写配置风险停住。不要再逐项询问用户是否写 AGENTS.md、是否初始化 .ac 工作目录、是否进入宿主工具安装引导；用户已经主动执行 setup，默认就是要做这些。不要把 planHash、approvedScopes、targetPath、executor、stub 这类内部词放在人读主线；不要让用户执行内部 Python 命令。
如果宿主工具缺失，summary.md 和 result.json 只是中间证据。当前 agent 不得结束本轮 setup 回复，必须按 host-tool-setup/references/host-tool-install-session.md 继续安装确认和执行：先说明将安装或配置什么、会写哪些用户级文件，按 _shared/references/subagent-precheck-protocol.md 完成 subagentPreReview 并确认材料可提交人工审查后，再等待用户确认；确认后执行；最后重新运行 verify 和 build-result。只有 verify 通过，才能说 GitNexus、Serena、Context7 或 MCP 可用。
© protect-my-hair, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Files
SKILL.md and 6 other files (scripts, references, assets) in plugins/nucleus/skills/setup of protect-my-hair/nucleus-marketplace.
- SKILL.md
- agents/openai.yaml
- assets/setup-summary-template.md
- references/human-result.md
- references/orchestration-boundary.md
- references/workflow-contract.md
- scripts/setup.py
Open the folder on GitHubat commit 3c82085
Compare with similar skills
Setup next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Setup this skillprotect-my-hair/nucleus-marketplace | 164 | — | ~1k | Automated safety check: Pass | MIT | |
| Bio Single Cell Hashing DemultiplexingGPTomics/bioSkills | 1.2k | 1 repos | ~4.2k | Automated safety check: Pass | MIT | |
| Bio Single Cell Cnv InferenceGPTomics/bioSkills | 1.2k | 1 repos | ~4.7k | Automated safety check: Pass | MIT | |
| Scenario Maya Fxscenario-labs/skills | 946 | — | ~5.3k | Automated safety check: Pass | MIT | |
| Cellpose Cell Segmentationjaechang-hits/SciAgent-Skills | 374 | 1 repos | ~3.5k | Automated safety check: Pass | BSD-3-Clause | |
| Game Concept ArchitectDY-2026/GameDesignOS | 415 | — | ~2.1k | Automated safety check: Pass | MIT |
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Questions about Setup
What does Setup do?
A skill your agent uses when 需要用一个 setup 入口完成 Nucleus 目标仓库初始化引导和宿主工具检查规划。. Setup is an agent skill from protect-my-hair/nucleus-marketplace.
When should I use Setup?
Setup fits situations like: 需要用一个 setup 入口完成 Nucleus 目标仓库初始化引导和宿主工具检查规划.
How do I install Setup in Claude Code?
Run `npx skills add protect-my-hair/nucleus-marketplace --skill setup -a claude-code`. Or copy the skill folder (plugins/nucleus/skills/setup in protect-my-hair/nucleus-marketplace) into .claude/skills/setup in your project. Claude Code loads it when a task matches its description.
How do I install Setup in Codex?
Run `npx skills add protect-my-hair/nucleus-marketplace --skill setup -a codex`. Or copy the skill folder (plugins/nucleus/skills/setup in protect-my-hair/nucleus-marketplace) into .agents/skills/setup in your project. Codex loads it when a task matches its description.
Can I use Setup in Cursor, Gemini CLI or GitHub Copilot?
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add protect-my-hair/nucleus-marketplace --skill setup -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/setup, .gemini/skills/setup, .github/skills/setup and .opencode/skills/setup in your project.
What does Setup need to run?
Going by SKILL.md and its folder, Setup needs Python for the scripts in its folder and the command-line tools its instructions call (python3). Our summary lists: Python 3.
Does Setup access the network?
SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.
Is Setup safe to install?
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.
What licence does Setup use?
Setup is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.
How many tokens does Setup use?
About 1k tokens (SKILL.md is roughly 4.1k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 1.3k tokens, read only when the agent opens those files.
What are the alternatives to Setup?
Skills that share tags, products or a category with Setup: Bio Single Cell Hashing Demultiplexing (GPTomics/bioSkills, 1.2k stars), Bio Single Cell Cnv Inference (GPTomics/bioSkills, 1.2k stars), Scenario Maya Fx (scenario-labs/skills, 946 stars) and Cellpose Cell Segmentation (jaechang-hits/SciAgent-Skills, 374 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Setup?
protect-my-hair (a GitHub user) maintains it in protect-my-hair/nucleus-marketplace, which has 164 GitHub stars. The repository holds 18 skills in this directory. The repository was last updated on July 23, 2026.
Source: protect-my-hair/nucleus-marketplace on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.