The Wegene Assistant MCP Server enables authorized users to access and analyze their WeGene genetic testing reports using an LLM. With this server, you can:
Authorize accounts: Start a WeGene Open API oAuth2 process to authorize a user's account and retrieve an access token
Retrieve profiles: Fetch the list of profiles associated with a user's WeGene account
Get report information: Retrieve metadata about all available genetic reports for a user
Access genetic reports: Fetch specific genetic test results from a profile using their endpoint, report ID, and profile ID
Click on "Install Server".
Wait a few minutes for the server to deploy. Once ready, it will show a "Started" state.
In the chat, type @ followed by the MCP server name and your instructions, e.g., "@Wegene Assistant MCP Server show me my genetic health risks report"
That's it! The server will respond to your query, and you can continue using it as needed.
Here is a step-by-step guide with screenshots.
MCP server for WeGene Assistant, using LLM to analyze a user's WeGene genetic testing report.
Once a user is authorized, all the reports under his/her account will be exposed as a resource:
Custom wegene:// URI scheme for accessing each individual report
A report resource has a name, description and application/json mimetype
The server implements one tool:
wegene-oauth: Start a WeGene Open API oAuth process in the browser
The user should complete the authorization in 120 seconds so LLM will be able to further access the reports.
wegene-get-profiles: Read the profile list under a user's WeGene account
Profiles' name and id will be returned for LLM to use.
wegene-get-report-info: Return the report meta info so LLM will know what reports are available.
A list of report names, descriptions, endpoints, etc. will be returned
wegene-get-report: Read the results of a single report under a profile
Returns the result JSON specified in WeGene's Open API platform
Arguements
report_endpoint: The report's endpoint to be retrieved from
report_id: The report's id to be retrieved
profile_id: The profile id to retrieve report from
Related MCP server: gwas-mcp
You will need WeGene Open API key/secret to use this project.
Copy .env.example as .env and update the key and secret in the file.
To install WeGene Assistant for Claude Desktop automatically via Smithery:
npx -y @smithery/cli install @xraywu/mcp-wegene-assistant --client claudeClone this project
Run uv sync --dev --all-extras under the project's root folder
On MacOS: ~/Library/Application\ Support/Claude/claude_desktop_config.json
On Windows: %APPDATA%/Claude/claude_desktop_config.json
Add below contents in the configuration file:
{
"mcpServers": {
"wegene-assistant": {
"command": "uv",
"args": [
"--directory",
"/path/to/wegene-assistant",
"run",
"wegene-assistant"
]
}
}
}Retrieve all the profiles under the current account
| Name | Required | Description | Default |
|---|---|---|---|
No parameters | |||
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
With no annotations provided, the description carries the full burden of behavioral disclosure. It states 'Retrieve all the profiles', implying a read-only operation, but doesn't specify details like whether it requires authentication (implied by 'current account'), rate limits, pagination, or what 'all' entails (e.g., scope or limitations). This leaves significant gaps in understanding the tool's behavior.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is a single, clear sentence that directly states the tool's purpose without any wasted words. It's front-loaded with the key action and resource, making it efficient and easy to parse for an agent.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Given the tool has 0 parameters, no annotations, and no output schema, the description is minimally adequate but incomplete. It explains what the tool does but lacks details on behavior (e.g., authentication needs, data format) and doesn't differentiate from siblings. For a simple retrieval tool, it meets basic needs but could benefit from more context.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
The tool has 0 parameters, and schema description coverage is 100%, so there's no need for parameter details in the description. The baseline for this scenario is 4, as the description doesn't need to compensate for missing param info, and it appropriately avoids unnecessary parameter explanations.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description clearly states the action ('Retrieve') and resource ('profiles under the current account'), making the purpose understandable. However, it lacks differentiation from sibling tools like 'wegene-get-report' or 'wegene-get-report-info', which might also retrieve data but for different resources, so it doesn't fully distinguish itself.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
The description provides no guidance on when to use this tool versus alternatives like 'wegene-get-report' or 'wegene-get-report-info'. It doesn't mention any prerequisites, exclusions, or specific contexts for usage, leaving the agent to infer based on tool names alone.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Get a specific genetic test report from a profile
| Name | Required | Description | Default |
|---|---|---|---|
| report_endpoint | Yes | The endpoint of the report | |
| report_id | Yes | The ID of the report | |
| profile_id | Yes | The ID of the profile |
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
No annotations are provided, so the description carries the full burden of behavioral disclosure. It states the tool 'Get's a report, implying a read operation, but doesn't cover aspects like authentication needs (though 'wegene-oauth' hints at this), rate limits, error handling, or what the output contains. This leaves significant gaps for a tool with no annotation coverage.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is a single, efficient sentence that directly states the tool's purpose without unnecessary words. It's front-loaded and appropriately sized for a simple retrieval tool, with no wasted information.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Given no annotations, no output schema, and three required parameters, the description is incomplete. It doesn't explain what the tool returns (e.g., report content format), authentication requirements (implied by sibling 'wegene-oauth'), or behavioral traits like error cases. For a tool with this complexity and lack of structured data, more context is needed.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema description coverage is 100%, so the schema already documents all three parameters (report_endpoint, report_id, profile_id) with basic descriptions. The description adds no additional meaning beyond implying these are needed to retrieve a report, aligning with the baseline score when the schema handles parameter documentation adequately.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description clearly states the action ('Get') and resource ('specific genetic test report from a profile'), making the purpose understandable. However, it doesn't differentiate from sibling tools like 'wegene-get-report-info' or 'wegene-get-profiles', which likely retrieve different types of genetic data or metadata.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
No guidance is provided on when to use this tool versus alternatives like 'wegene-get-report-info' or 'wegene-get-profiles'. The description implies usage for retrieving a report but doesn't specify contexts, prerequisites, or exclusions, leaving the agent to infer based on tool names alone.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Get all available report information
| Name | Required | Description | Default |
|---|---|---|---|
No parameters | |||
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
With no annotations provided, the description carries full burden for behavioral disclosure. It states this is a 'Get' operation, implying read-only behavior, but doesn't specify authentication needs, rate limits, error conditions, or what 'all available report information' entails (e.g., format, scope, or limitations). This leaves significant gaps for a tool with no annotation coverage.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is a single, efficient sentence that directly states the tool's purpose without any fluff or redundancy. It's appropriately sized for a zero-parameter tool and front-loads the essential information clearly.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Given the lack of annotations and output schema, the description is incomplete. It doesn't explain what 'report information' includes, how it's structured, or any behavioral aspects like authentication or errors. For a tool that likely returns data, more context is needed to guide the agent effectively.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
The tool has zero parameters, and schema description coverage is 100%, so there's no need for parameter documentation in the description. The description appropriately doesn't discuss parameters, aligning with the schema's empty properties. A baseline of 4 is given since no parameters exist, and the description doesn't add unnecessary details.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description clearly states the action ('Get') and resource ('all available report information'), making the purpose understandable. However, it doesn't differentiate this tool from its sibling 'wegene-get-report', leaving some ambiguity about what distinguishes 'report information' from just 'report'.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
The description provides no guidance on when to use this tool versus alternatives like 'wegene-get-report' or 'wegene-get-profiles'. There's no mention of prerequisites, context, or exclusions, leaving the agent with no usage direction beyond the basic purpose.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Authorizing a user's account using WeGene Open API with oAuth2 protocol and retrieve a valid access token for further use
| Name | Required | Description | Default |
|---|---|---|---|
No parameters | |||
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
No annotations are provided, so the description carries the full burden of behavioral disclosure. It mentions oAuth2 protocol and token retrieval, which implies authentication and potential user interaction, but doesn't detail behavioral traits such as whether this initiates a user consent flow, requires specific permissions, involves rate limits, or handles errors. For an authentication tool with zero annotation coverage, this leaves significant gaps in understanding how it behaves.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is a single, well-structured sentence that efficiently conveys the core functionality without unnecessary details. It is front-loaded with the main action and outcome, making it easy to understand quickly. Every word earns its place, and there is no wasted information.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Given the tool's complexity (authentication with oAuth2), lack of annotations, and no output schema, the description is minimally adequate. It explains what the tool does but doesn't cover important contextual details like the token's scope, expiration, or how to use it with sibling tools. For an authentication tool, more completeness is expected to guide proper integration.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
The input schema has 0 parameters with 100% coverage, meaning there are no parameters to document. The description doesn't need to add parameter semantics, so it appropriately focuses on the tool's purpose. A baseline of 4 is applied since no parameters exist, and the description doesn't mislead about inputs.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description clearly states the tool's purpose: 'Authorizing a user's account using WeGene Open API with oAuth2 protocol and retrieve a valid access token for further use.' It specifies the action (authorizing via oAuth2) and the outcome (retrieving an access token). However, it doesn't explicitly distinguish this from its siblings (e.g., wegene-get-profiles, wegene-get-report), which focus on data retrieval rather than authentication.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
The description implies usage by stating the token is 'for further use,' suggesting this tool should be invoked before other tools that require authentication. However, it doesn't provide explicit guidance on when to use it versus alternatives (e.g., if re-authentication is needed) or any prerequisites. The context is clear but lacks detailed exclusions or comparisons.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Recent tool additions, removals, and schema changes observed during successful MCP inspections. Dates show when Glama detected each change.
wegene-get-profileswegene-get-reportwegene-get-report-infowegene-oauthEach tool has a clearly distinct purpose: get-profiles retrieves account profiles, get-report fetches a specific genetic report, get-report-info lists available reports, and oauth handles authentication. There is no overlap in functionality, making tool selection unambiguous.
All tools follow a consistent 'wegene-verb-noun' pattern with hyphens, using clear verbs like 'get' and 'oauth'. This uniformity makes the tool set predictable and easy to understand.
Four tools are reasonable for a genetic data server, covering authentication, profile retrieval, and report access. It might benefit from additional operations like updating profiles or deleting data, but the core scope is well-defined.
The tools cover authentication and read operations (profiles and reports) adequately, but there are notable gaps in write operations such as creating, updating, or deleting profiles or reports. This limits the server to read-only workflows.
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