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Skillsdym-scientific-agent-skills-cai-dat-skills

dym-scientific-agent-skills-cai-dat-skills

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Updated 10-18 01:22

About this skill

Skill: dym-scientific-agent-skills-cai-dat-skills — Install Scientific Agent Skills into your agent

Why use it: bring a subset of the 163 scientific skills into the agent (Claude Code / Cursor / Codex / Gemini CLI / Antigravity…) so it has ready-made workflows for bioinformatics, cheminformatics, database lookup, scientific paper writing… What it produces: the directories <skill-name>/SKILL.md (along with references/, scripts/, assets/ if any) located in the host's skill directory, plus traceable metadata inserted into the frontmatter.

⚠️ Run 02-tham-dinh-truoc-khi-cai.md first. The repo itself recommends not installing the whole set, and 16/163 skills currently carry CRITICAL/HIGH findings in their scan report.

Path A — npx skills (recommended, supports selecting a subset)

See what the repo has without installing anything:

npx -y skills add K-Dense-AI/scientific-agent-skills --list

Actually ran: printed Found 163 skills then listed each skill along with description. This command clones the repo into a temporary cache, without writing to the skill directory.

Install just the few skills you need (this is the way you should use):

# project scope (mặc định) — cài vào dự án hiện tại
npx -y skills add K-Dense-AI/scientific-agent-skills -s "depmap,paper-lookup,database-lookup" -y

# user scope — dùng được ở mọi dự án
npx -y skills add K-Dense-AI/scientific-agent-skills -g -s "depmap,paper-lookup" -y

# chỉ định host cụ thể
npx -y skills add K-Dense-AI/scientific-agent-skills -a claude-code -s "depmap" -y

Flags verified via npx skills@1.5.23 --help:

Flag Meaning
-s, --skill <skills> select skills (use '*' for all)
-a, --agent <agents> select host (use '*' for all)
-g, --global user scope instead of project scope
-l, --list list only, don't install
--copy copy files instead of symlinking into the agent directory
-y, --yes skip prompt
--all abbreviation of --skill '*' --agent '*' -y — don't use with this repo

Want to try a skill without installing anything:

npx -y skills use K-Dense-AI/scientific-agent-skills@depmap

Path B — gh skill (GitHub CLI ≥ 2.90, has provenance)

# xem nội dung SKILL.md trước, không cài
gh skill preview K-Dense-AI/scientific-agent-skills depmap

# cài một skill cho Claude Code, phạm vi project
gh skill install K-Dense-AI/scientific-agent-skills depmap --agent claude-code --scope project

# phạm vi user
gh skill install K-Dense-AI/scientific-agent-skills depmap --agent claude-code --scope user

# đích tuỳ ý (bỏ qua --agent/--scope)
gh skill install K-Dense-AI/scientific-agent-skills depmap --dir ./vendor/skills

Actual file location — ran and observed, in an empty git repo:

--agent claude-code --scope project  →  .claude/skills/depmap/{SKILL.md,references/}
--agent cursor       --scope project  →  .agents/skills/depmap/{SKILL.md,references/}

.agents/skills is the directory shared by many hosts (GitHub Copilot, Cursor, Codex, Gemini CLI, Antigravity, Amp, Cline, OpenCode, Warp). If you select multiple hosts that all point there, the skill exists in only one copy.

Actual output of the install command (exit 0):

Using ref v2.66.0 (1e5eeffb)
✓ Installed depmap (from K-Dense-AI/scientific-agent-skills@v2.66.0) in ...
  depmap/
  ├── SKILL.md
  └── references/
      └── dependency_analysis.md

When no version is passed, gh resolves the version in order: (1) latest release tag, (2) HEAD of the default branch. To pin a version see 05-pin-va-cap-nhat.md.

Three pitfalls of Path B

  • --agent gemini in the repo README is wrong. The correct value is gemini-cli. The valid list is in gh skill install --help.
  • Non-interactive requires a skill name. The README says gh skill install K-Dense-AI/scientific-agent-skills is "browse interactively" — only true in an interactive terminal. In CI or when an agent calls it, a missing skill name is an error.
  • The repo with 163 skills would be very slow to traverse the tree if you only give a name. Pass the exact path to skip the full-tree traversal step:
gh skill install K-Dense-AI/scientific-agent-skills skills/depmap

Path C — Agent Plugins / manual clone (get the full set)

The repo root is a valid Agent Plugins 1.0.0 package (plugin.json + skills/). Clients that support this standard will detect every direct subdirectory of skills/ that has SKILL.md.

# Cursor
mkdir -p ~/.cursor/plugins/local
git clone https://github.com/K-Dense-AI/scientific-agent-skills.git \
  ~/.cursor/plugins/local/scientific-agent-skills
# rồi Developer: Reload Window

# Host quét ~/.agents/skills (user-level)
git clone https://github.com/K-Dense-AI/scientific-agent-skills.git \
  ~/.agents/skills/scientific-agent-skills

# project-level
git clone https://github.com/K-Dense-AI/scientific-agent-skills.git \
  .agents/skills/scientific-agent-skills

This path loads all 163 skills. The entire skills/ tree weighs 28 MB and every SKILL.md resides permanently in the agent's context — the repo itself recommends "consider installing a subset by topic instead of the whole set". You should only use path C when you actively want all of them.

Check after installation

# skill nào đang cài (nếu dùng npx skills)
npx -y skills list

# đọc lại đúng file agent sẽ nạp
ls .claude/skills/ .agents/skills/ 2>/dev/null
head -20 .claude/skills/depmap/SKILL.md

In the agent: ask directly "do you have the depmap skill, describe it" — if the host has loaded it, it must be able to read description in the frontmatter.

Environment requirements

  • Python 3.13+ for the repo tooling; individual skills may accept a wider Python range.
  • uv — many skills instruct installing dependencies with uv. Check with uv --version; if not present, install per Astral's official instructions. (The machine running this bundle does not have uv; every verify step therefore used a plain Python 3.13 venv — see 08.)
  • Host: any agent following the Agent Skills standard.
  • OS: macOS, Linux, or Windows + WSL2.