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reproducible-pipelines

80 / 100 · Low risk

Fine to try.

By brycewang-stanford/Auto-Empirical-Research-Skills (GitHub) · research · 5,016 stars · scanned at commit 8684584

This skill covers reproducible research pipelines and replication packages. Use when the user is setting up a research project directory structure, configuring workflow managers (Make, Snakemake, DVC), managing computational environments, preparing replication packages for journal submission, or debugging reproducibility failures. Triggers on "reproducible", "replication package", "Makefile", "Snakemake", "DVC", "pipeline", "workflow manager", "data versioning", "conda environment", "Docker", "…

Works with any agent that supports SKILL.md skills.

What this skill can do

Install

Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.

if [ -e ~/.agents/skills/'reproducible-pipelines' ] || [ -L ~/.agents/skills/'reproducible-pipelines' ]; then echo 'A skill folder named reproducible-pipelines already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills' "$d" && git -C "$d" checkout --quiet '8684584e7d1127940f018157d2c579974fae8f79' -- 'skills/11-James-Traina-compound-science/skills/reproducible-pipelines' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/11-James-Traina-compound-science/skills/reproducible-pipelines' ~/.agents/skills/'reproducible-pipelines' && rm -rf "$d"; fi

Codex reads ~/.agents/skills directly. For Claude Code, Cursor, Copilot, Gemini CLI, Antigravity or OpenCode, also link it. For Claude Code: ln -s ~/.agents/skills/'reproducible-pipelines' ~/.claude/skills/'reproducible-pipelines' (other agents: ~/.cursor/skills, ~/.copilot/skills, ~/.gemini/skills, ~/.gemini/config/skills, ~/.config/opencode/skills). Or install through the finder skill, which does both.

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