metadome-link
Server Configuration
Describes the environment variables required to run the server.
| Name | Required | Description | Default |
|---|---|---|---|
| METADOME_LINK_HOST | No | Bind host. | 0.0.0.0 |
| METADOME_LINK_PORT | No | Bind port. | 8000 |
| METADOME_LINK_MCP_PATH | No | MCP endpoint path. | /mcp |
| METADOME_LINK_LOG_LEVEL | No | DEBUG…CRITICAL. | INFO |
| METADOME_LINK_TRANSPORT | No | unified | http | stdio. | unified |
| METADOME_LINK_LOG_FORMAT | No | console | json (logs to stderr only). | console |
| METADOME_LINK_CORS_ORIGINS | No | Comma-separated allowed CORS origins. | |
| METADOME_LINK_CACHE__DB_PATH | No | On-disk result cache path. | data/metadome_cache.sqlite |
| METADOME_LINK_CACHE__LRU_RESULTS | No | In-memory LRU size for completed landscapes. | 64 |
| METADOME_LINK_METADOME__BASE_URL | No | Override upstream base URL. | |
| METADOME_LINK_METADOME__MAX_RETRIES | No | Retries on 429/5xx/timeout. | 3 |
| METADOME_LINK_CACHE__LRU_TRANSCRIPTS | No | In-memory LRU size for transcript lists. | 256 |
| METADOME_LINK_CACHE__TTL_TRANSCRIPTS_S | No | TTL for transcript list cache (default 6 h). | 21600 |
| METADOME_LINK_METADOME__POLITENESS_BURST | No | Token-bucket burst capacity. | 5 |
| METADOME_LINK_METADOME__REQUEST_TIMEOUT_S | No | Per-request HTTP timeout (s). | 30.0 |
| METADOME_LINK_METADOME__POLL_MAX_INTERVAL_S | No | Maximum inter-poll sleep (s). | 8.0 |
| METADOME_LINK_METADOME__POLL_SOFT_DEADLINE_S | No | Max poll-loop wall time before returning status:'processing'. | 20.0 |
| METADOME_LINK_METADOME__POLITENESS_RATE_PER_S | No | Token-bucket refill rate (req/s). | 3.0 |
| METADOME_LINK_METADOME__POLL_INITIAL_INTERVAL_S | No | Initial poll sleep (s); backs off toward max. | 2.0 |
Instructions
Guidance the server publishes about itself, which clients place ahead of the tool catalog so the model reads it before choosing anything.
This server publishes no instructions, or was last inspected before Glama recorded them.
Capabilities
Features and capabilities supported by this server
Protocol revision2025-11-25
| Capability | Details |
|---|---|
| tools | {
"listChanged": true
} |
| logging | {} |
| prompts | {
"listChanged": false
} |
| resources | {
"subscribe": false,
"listChanged": false
} |
| extensions | {
"io.modelcontextprotocol/ui": {}
} |
| experimental | {} |
Tools
Functions exposed to the LLM to take actions
| Name | Description |
|---|---|
| get_server_capabilitiesD | Signature: get_server_capabilities(detail=, response_mode=). |
| get_diagnosticsD | Signature: get_diagnostics(response_mode=). |
| resolve_transcriptD | Signature: resolve_transcript(query, response_mode=). |
| request_tolerance_landscapeD | Signature: request_tolerance_landscape(transcript_id, response_mode=). |
| get_tolerance_landscapeD | Signature: get_tolerance_landscape(transcript_id, position_start=, position_stop=, limit=, offset=, response_mode=). |
| get_position_toleranceD | Signature: get_position_tolerance(transcript_id, position, response_mode=). |
| get_variant_countsD | Signature: get_variant_counts(transcript_id, position=, position_start=, position_stop=, source=, limit=, offset=, response_mode=). |
| compare_positionsD | Signature: compare_positions(transcript_id, positions, response_mode=). |
| get_protein_domainsD | Signature: get_protein_domains(transcript_id, response_mode=). |
| get_meta_domainD | Signature: get_meta_domain(transcript_id, position, domains=, limit=, offset=, response_mode=). |
| summarize_intolerant_regionsD | Signature: summarize_intolerant_regions(transcript_id, threshold=, min_run=, top_n=, response_mode=). |
Prompts
Interactive templates invoked by user choice
| Name | Description |
|---|---|
No prompts | |
Resources
Contextual data attached and managed by the client
| Name | Description |
|---|---|
| capabilities | |
| tools_overview | |
| usage | |
| reference | |
| research_use | |
| citation |
TDQS
Scored across 11 tools
Tools are largely distinct with clear purposes. The async request/get pair for tolerance landscapes is well-defined, and get_tolerance_landscape vs get_position_tolerance differ by range granularity. Minor potential overlap between get_protein_domains and get_meta_domain could cause occasional misselection, but descriptions clarify.
Naming follows a consistent pattern: get_ for retrieval, request_ for initiating asynchronous operations, and resolve_ for transcript mapping. All snake_case with clear resource nouns. No mixed conventions or vague verbs.
11 tools is well-scoped for a variant tolerance analysis server. Each tool serves a distinct purpose without redundancy, and the count aligns with the domain's complexity.
The surface covers the full workflow: capabilities, diagnostics, transcript resolution, landscape retrieval (async and sync), positional tolerance, variant counts, comparison, domain annotations, and summary analysis. No obvious gaps for a read-only analysis server.