Detect outdated tools in Bactopia modules and update module.config and CHANGELOG.md.
npx skills add https://github.com/bactopia/bactopia --skill update-module
Please help me install this Agent Skill. Skill: update-module Source: https://github.com/bactopia/bactopia/tree/main/.claude/skills/update-module Command: npx skills add https://github.com/bactopia/bactopia --skill update-module
The Skill automates the process of identifying newer versions of tools used in Bactopia modules and applying updates to module.config files and CHANGELOG.md, reducing manual maintenance overhead.
Run the wrapper script to scan for outdated tools and apply selected updates to module.config files and CHANGELOG.md.
High-intent search queries and answers about installing and using this skill.
To auto-update Bactopia module.config files, run the bactopia-update wrapper to identify newer tool versions and batch apply changes to ext.toolName, ext.docker, and ext.image fields, while flagging manual review cases.
Automating CHANGELOG.md updates for Bactopia modules involves recording applied tool version changes under the Unreleased Changes section with proper formatting and deduplication of tools, handled automatically by the update script.
Bactopia detects outdated module tools by scanning module.config files for newer versions, then applies updates to ext.toolName, ext.docker, and ext.image fields while generating a clean summary for review before committing changes.
Yes, you need conda and python3 installed as dependencies to run the bactopia-update script, which scans for outdated tools and applies version updates to module.config files and CHANGELOG.md.
The best way to track manual review cases during Bactopia module updates is using the auto-detection feature, which flags review cases while batch updating ext.toolName, ext.docker, and ext.image fields in module.config files.
Yes, you can batch update ext.toolName, ext.docker, and ext.image fields across Bactopia modules by running the update wrapper, which applies newer tool versions and records changes in CHANGELOG.md with deduplication.
bactopiaScaffold Bactopia modules from Bioconda packages with standard files and tests.
Unique-AGUpdate CHANGELOG.md and pyproject.toml versions from commit history.
bactopiaScaffolds a complete Bactopia Tool pipeline from a bioconda package.
bactopiaRegenerate Bactopia catalog.json and llms.txt via bactopia-catalog.
