Agents and skills¶

Claude Code skills and agents¶

Every analysis module comes with a Claude Code skill that teaches Claude to use it: what to ask you before running anything, the real defaults, and how to read the outputs. Modules whose use is a long multi-step job can also get an agent. Install them one of two ways, not both (with both, every skill is listed twice):

With the package, so the skills match the version you have installed:

cau install-skills                   # into ~/.claude (or $CLAUDE_CONFIG_DIR)
cau install-skills --target .claude  # into the current project only
cau install-skills --list            # what is bundled

After upgrading the package, run it again with --force.

As a Claude Code plugin, which follows the main branch:
```
/plugin marketplace add EngreitzLab/crispr-analysis-utils
/plugin install crispr-analysis-utils@crispr-analysis-utils
```
Update it with /plugin marketplace update crispr-analysis-utils, or add the marketplace as EngreitzLab/crispr-analysis-utils#<tag> to follow a tag instead of main.

What ships¶

Skill	Covers
`cau-accession`	`cau.accession`: accession ids for SpCas9 guides, encoded from the guide's own sequence
`cau-normalization`	`cau.counts_per_million`
`cau-guide-alignment`	`cau.guide_alignment` and the `cau guide-alignment` command: finding every guide's genomic site, and reading the outputs
`cau-igvf-export`	`cau.igvf_export` and the `cau igvf-export` command: writing a guide design in the IGVF per-guide metadata format
`cau-element-mapping`	`cau.element_mapping` and the `cau element-mapping` command: mapping guides to a screen's elements, and checking a design's control sets
`cau-guide-annotation`	`cau.guide_annotation` and the `cau guide-annotation` command: building the GENCODE store, placing sites in genes, and reading the output

cau install-skills --list prints the same list from the installed package.

Skill or agent¶

Every analysis module has a skill. A skill loads into your conversation, so you see and steer each step: it suits a module whose use is a matter of knowing the functions and choosing the parameters.

An agent is added when using a module means a long multi-step job (run a pipeline, read its logs, summarize the outcome) whose intermediate output would flood the conversation. The agent works in its own context and returns a summary. It preloads the module's skill rather than repeating it, so the module still has exactly one description of how it works.

Where they live¶

The skills ship inside the Python package, under crispr_analysis_utils/skills/<name>/SKILL.md, and agents under crispr_analysis_utils/agents/. cau install-skills copies them from the installed package. The plugin serves the same directory straight from the repository's main branch.