claude_skill

Claude Skill (AI agent integration)

SQANTI-browser ships a Claude Agent Skill — a bundle of instructions that teaches an AI coding agent (e.g. Claude Code) how to use SQANTI-browser correctly: the right command and flags, required inputs, the track-hub output, hosting and hubCheck validation, UCSC filtering and Trix search, isoform ordering, custom palettes, non-reference genomes, curated subset sessions, and SQANTI-reads workflows. Once installed, you can just describe what you want in plain language and the agent builds and validates the hub for you.

This mirrors the approach used by packages like decoupler.

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Requirements

• Claude Code (or another agent that loads Agent Skills from ~/.claude/skills/).
• SQANTI-browser installed (see Installation) — the skill ships inside the package.
• The UCSC command-line tools on your PATH for the agent to actually build hubs (gtfToGenePred, genePredToBed, bedToBigBed, plus twoBitInfo/ixIxx as needed). The skill can install these for you, but they must be available at run time.

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Install the skill

After installing SQANTI-browser, run the bundled installer once:

pip install sqanti-browser          # or, from a clone: pip install -e .
sqanti-browser-install-skills

This copies the skill into ~/.claude/skills/sqanti-browser/, making it available in every project. Start a new agent session to pick it up.

After upgrading SQANTI-browser, re-run with --force to refresh the installed copy:

sqanti-browser-install-skills --force

Custom skills location. If you keep your skills somewhere other than ~/.claude/skills, point your agent at the bundled files without copying:

export CLAUDE_SKILLS_PATH="$(sqanti-browser-install-skills --print-path)"

--print-path prints the bundled skill directory and exits without installing.

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Verify it's installed

ls ~/.claude/skills/sqanti-browser/SKILL.md

In a new Claude Code session, mention SQANTI-browser (for example, "build a UCSC hub from my SQANTI3 output") and the agent will load the skill automatically.

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What the skill knows

The skill is a short router (SKILL.md) plus focused reference files:

Topic	Reference
Every flag, default, and choice	cli-reference.md
Required/optional inputs and the hub output tree	inputs-outputs.md
Installing the tool + UCSC utilities	installation.md
Hosting the hub and loading it in UCSC (hubCheck)	hosting.md
Interactive HTML tables (--tables)	html-tables.md
UCSC filtering and Trix search	filtering-and-search.md
Isoform ordering (--sort-by)	isoform-ordering.md
Custom colors (--my-palette)	custom-coloring.md
Non-reference genomes (--twobit)	non-reference-genomes.md
Curated subset sessions	subset-sessions.md
Multi-sample SQANTI-reads workflows	sqanti-reads-integration.md
Diagnosing errors	troubleshooting.md

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Example prompts

• "Build a UCSC track hub from corrected.gtf and classification.txt for hg38."
• "Add CAGE and polyA validation tracks and a reference GTF, and generate the HTML tables."
• "Make a hub for my SIRV spike-ins from this .2bit file."
• "Sort isoforms by full-length read count and only keep FSM, ISM, and NIC category tracks."
• "Validate my hub with hubCheck and tell me what's wrong."
• "Set up one hub per sample for my SQANTI-reads experiment so I can compare them in UCSC."

The agent runs read-only diagnostics freely and will ask before anything destructive or long-running.

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Updating and removing

• Update: upgrade the package, then sqanti-browser-install-skills --force.
• Remove: delete the folder: rm -rf ~/.claude/skills/sqanti-browser.

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Other agents

The skill is a standard Agent Skill directory (SKILL.md + references/ + assets/), so any agent that reads that format can use it. Use sqanti-browser-install-skills --print-path to locate the bundled files, then copy or symlink them into your agent's skills directory.

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See Also

• Installation
• Command Line Reference
• Usage Examples
• Hosting Guide