MGnify MCP Server
Server Configuration
Describes the environment variables required to run the server.
| Name | Required | Description | Default |
|---|---|---|---|
| BIND | No | Only used if you enable the HTTP transport in server.py | |
| PORT | No | Only used if you enable the HTTP transport in server.py | |
| MG_API_KEY | No | If you have an API token, it will be sent as Bearer auth | |
| MG_BASE_URL | No | Override the MGnify API base URL | https://www.ebi.ac.uk/metagenomics/api/v1 |
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": false
} |
| prompts | {
"listChanged": false
} |
| resources | {
"subscribe": false,
"listChanged": false
} |
| experimental | {} |
Tools
Functions exposed to the LLM to take actions
| Name | Description |
|---|---|
| mgnify_list_biomesA | List biomes (environmental categories like soil, marine, gut). Filter by |
| mgnify_list_studiesA | Search MGnify studies. Filters: |
| mgnify_get_studyB | Get a single study by MGnify accession (e.g. 'MGYS00005292'). Returns title, biome, metadata. |
| mgnify_study_samplesC | List samples that belong to a study. |
| mgnify_study_analysesC | List analyses produced from a study. |
| mgnify_study_publicationsA | List publications linked to a study. |
| mgnify_list_super_studiesC | List super-studies (umbrella collections like Tara Oceans, Earth Microbiome Project, HoloFood). |
| mgnify_get_super_studyA | Get a super-study by url-slug (e.g. 'tara-oceans', 'earth-microbiome-project', 'holofood'). Response embeds flagship_studies, related_studies, and genome_catalogues. |
| mgnify_list_samplesA | Search samples. Filters: |
| mgnify_get_sampleB | Get one sample by accession (e.g. 'ERS123456'). Returns title, biome, metadata, related studies. |
| mgnify_sample_runsB | List sequencing runs taken from a sample. |
| mgnify_list_runsA | List sequencing runs. Filter by |
| mgnify_get_runC | Get one run by accession (e.g. 'ERR1234567'). |
| mgnify_run_analysesB | List analyses produced from a single run. |
| mgnify_list_analysesA | List MGnify analyses. The v2 /analyses/ endpoint supports only pagination — use mgnify_study_analyses or mgnify_run_analyses for filtered lookups. |
| mgnify_get_analysisB | Get one analysis by MGnify accession (e.g. 'MGYA00012345'). Includes pipeline_version, downloads, results_dir. |
| mgnify_analysis_annotationsB | Fetch a typed annotation table for an analysis. annotation_type must be one of: taxonomies__ssu, taxonomies__lsu, taxonomies__its_one_db, taxonomies__unite, taxonomies__pr2, taxonomies__dada2_pr2, taxonomies__dada2_silva, pfams. Pick taxonomies__ssu for 16S/18S ribosomal taxonomy, pfams for protein-family annotation. |
| mgnify_list_genome_cataloguesA | List MGnify genome catalogues (e.g. human-gut, marine, chicken-gut). Returns catalogue_id, name, biome label, genome_count, pipeline_version_tag, catalogue_type. |
| mgnify_get_genome_catalogueC | Get one genome catalogue by id (e.g. 'human-gut-v2-0-2', 'marine-v2-0'). |
| mgnify_list_genomesA | List genomes inside a catalogue. Provide catalogue_id (e.g. 'human-gut-v2-0-2'); v2 only exposes genomes scoped to a catalogue. |
| mgnify_get_genomeA | Get one genome by MGnify accession (e.g. 'MGYG000000001'). Returns length, completeness, taxon_lineage, etc. |
| mgnify_list_publicationsC | Search publications. Filters: |
| mgnify_get_publicationA | Get one publication by PubMed id. |
Prompts
Interactive templates invoked by user choice
| Name | Description |
|---|---|
| explain_mgnify_plan |
Resources
Contextual data attached and managed by the client
| Name | Description |
|---|---|
| res_biomes | |
| res_catalogues | |
| res_super_studies |
TDQS
Scored across 23 tools
Every tool targets a distinct entity or relationship: list/get variants for studies, samples, runs, analyses, genomes, catalogues, publications, biomes, and super-studies. Where multiple tools list analyses, their scoping (all, by study, by run) is explicit in descriptions, so an agent should not confuse them.
The set consistently uses the mgnify_ prefix and snake_case, with list_X/get_X for most resources. The relational endpoints (mgnify_study_analyses, mgnify_sample_runs) and the single mgnify_analysis_annotations deviate from the list/get convention, but the pattern is still predictable.
23 tools is above the typical sweet spot, but the domain spans many entity types and each tool maps to a distinct API operation. It is slightly heavy but not bloated.
The read-only domain is covered end-to-end: every core entity has a list and get tool, and relationship tools allow traversal from super-studies/studies to samples to runs to analyses, plus genome catalogues and publications. No obvious dead ends or missing operations for the stated browse/search purpose.