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dna-seq
by dna-seq

List genomes

list_genomes
Read-onlyIdempotent

Discover available genomes in the cache: list downloaded VCFs, normalized Parquets, and pre-configured samples for scoring or comparison. Reads local filesystem only.

Instructions

List genomes available in the server's cache directory.

Scans <cache_dir>/samples/ for downloaded raw VCF files and <cache_dir>/normalized/ for normalized Parquet files. Also lists the pre-configured sample genomes that can be downloaded via download_sample_genome (even if not yet downloaded).

Use this to discover genomes you can score or compare (Anton + Livia are the built-in pair):

  • Which genomes have already been downloaded (ready for direct scoring).

  • Which genomes have already been normalized (ready for compute_prs / compute_prs_by_trait as an optional reusable fast path).

  • Which pre-configured samples are available for download.

No network access required — reads the local filesystem only.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault

No arguments

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
messageYesHuman-readable summary.
cache_dirYesRoot cache directory path.
downloadedNoRaw VCF files in <cache_dir>/samples/.
normalizedNoNormalized Parquet files in <cache_dir>/normalized/.
available_samplesNoPre-configured sample genomes that can be downloaded via download_sample_genome (name, description, size, license).
Install Server

TDQS

A4.5/5.0
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

The description goes beyond the annotations by stating it does a local filesystem scan, reads specific directories, and has no network access. It also explains that it lists pre-configured samples even if not downloaded, which is a behavioral nuance. The annotations (readOnlyHint, idempotentHint, destructiveHint) are consistent and the description adds detail about what it inspects. However, it doesn't describe output format or pagination, but given the annotations cover safety, this is adequate.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is a well-structured paragraph with bullet-like points in prose. It's concise, using clear sections and specific file paths. Every sentence adds value—explains what it scans, what it lists, and its network behavior. No fluff. Slightly verbose with the bulleted hints but still efficient.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given the tool has no parameters and an output schema (not detailed here), the description explains the sources and purpose well. It mentions key use cases (scoring, comparison), but does not explicitly describe the output structure since that is provided by the output schema. It is complete for the tool's simple nature. It could mention if it returns any errors or edge cases, but that's not critical. Overall, it's well-rounded.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

There are 0 parameters, so schema coverage is 100% trivially. The description adds no parameter-specific info because none exist, but it does explain the scope of what is listed (cache dirs, pre-configured samples). Since there are no parameters, a baseline of 4 is appropriate as the description provides context about the tool's operation without needing to explain parameters.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states the verb+resource: 'List genomes available in the server's cache directory.' It specifies the exact directories scanned and the distinction between downloaded, normalized, and pre-configured sample genomes. It also differentiates from siblings like compare_genomes and download_sample_genome by explicitly mentioning the built-in pair and the purpose.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines5/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description explicitly states when to use this tool: 'Use this to discover genomes you can score or compare' and lists what to look for (downloaded, normalized, pre-configured). It also provides an exclusion: 'No network access required — reads the local filesystem only,' implying it's not for network operations. The mention of alternative tools (download_sample_genome, compute_prs, etc.) in the context implies when to use this instead.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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