Use mintyr with AI agents

Source: vignettes/articles/agent-skill.Rmd

中文版

mintyr-pipelines is an Agent Skill: a SKILL.md file that teaches an AI agent how to use mintyr. With it installed, you can ask in plain language, for example:

  • “Combine these Excel files and give me mean ± SD of ADG and backfat by breed, with a total row.”
  • “Nest the data by trait and farm, run 5-fold cross-validation, and report the mean accuracy per group.”
  • “Write one phenotype file per trait for DMU, with -9999 for missing values and no header.”

The agent then installs mintyr if needed, writes an R script, runs it, checks the result and hands you the files (and the script, so you can rerun it).

Download

Language ZIP (Claude, other agents) Instructions (Claude Code, reading)
English mintyr-pipelines.zip SKILL.md
Chinese mintyr-pipelines-zh.zip SKILL.md

Both versions do the same thing; the language only affects the instructions the agent reads, not the language it answers in. Install one of them: with both installed, the agent has two overlapping skills to choose from.

Skills run code on your behalf, so read SKILL.md before installing it.

Requirements

The agent must be able to run commands and reach an R installation. The skill installs mintyr itself, in this order:

  1. from CRAN (install.packages("mintyr")), if CRAN is reachable;
  2. otherwise R and the dependencies from apt (Ubuntu / Debian) and mintyr from GitHub source.

So the agent’s network must allow CRAN (cloud.r-project.org) or GitHub (github.com). If mintyr is already installed, no network is needed.

Install in Claude (web and desktop app)

Custom skills are available on the Pro, Max, Team and Enterprise plans.

  1. Download mintyr-pipelines.zip (or the Chinese mintyr-pipelines-zh.zip). Do not unzip it.
  2. In Claude, open Settings › Capabilities and turn on code execution and file creation (skills need it).
  3. In the Skills section, click Upload skill and select the ZIP file. Make sure the skill is switched on.
  4. Allow the network access the skill needs: in the allowed domains on the same page, add github.com (and cloud.r-project.org if you can). On Team and Enterprise plans an admin sets this under Organization settings › Capabilities, and on Enterprise an owner must first enable skills.

Then start a new chat, attach your data files and describe the task.

Install in Claude Code

Personal skill, available in all your projects (macOS / Linux):

mkdir -p ~/.claude/skills/mintyr-pipelines
curl -fsSL https://raw.githubusercontent.com/tony2015116/mintyr/main/.claude/skills/mintyr-pipelines/SKILL.md \
  -o ~/.claude/skills/mintyr-pipelines/SKILL.md

Windows (PowerShell):

New-Item -ItemType Directory -Force "$HOME\.claude\skills\mintyr-pipelines" | Out-Null
Invoke-WebRequest "https://raw.githubusercontent.com/tony2015116/mintyr/main/.claude/skills/mintyr-pipelines/SKILL.md" `
  -OutFile "$HOME\.claude\skills\mintyr-pipelines\SKILL.md"

For the Chinese version, replace mintyr-pipelines with mintyr-pipelines-zh in the folder names and the URL.

For a single project, put the file at <project>/.claude/skills/mintyr-pipelines/SKILL.md instead and commit it, so everyone on the project gets it. A clone of the mintyr repository already contains both versions.

Claude Code uses the R installed on your computer, so installing mintyr there first (install.packages("mintyr")) saves time.

Other agents and the Claude API

SKILL.md follows the open Agent Skills format. For other agents that support it, unzip mintyr-pipelines.zip (or mintyr-pipelines-zh.zip) into the folder where that agent reads skills (see its documentation). With the Claude API, upload the folder as a custom skill as described in the skills guide.

Agent platforms that do not support skills can still use the content: paste SKILL.md into the agent’s instructions, as long as the agent can run R code.

Updating

The skill is updated together with mintyr. To update, download the ZIP or SKILL.md again and replace the old copy (in Claude: delete the old skill, then upload the new ZIP).