How to Use the Ensembl MCP in Claude Code

Q: How do I configure Claude Code for Ensembl?

Run claude mcp add --transport http ensembl-mcp -- . Ensure all flags come before the server name. Claude Code stores this configuration in your /.claude.json file.

Q: Can Claude Code pipe Ensembl sequence data to other CLI tools?

Yes. You can ask the agent to fetch a sequence via getsequenceregion and output it as standard text. You then pipe that directly into tools like BLAST or grep right in your shell.

Q: How do I verify the connection is actively running?

Run claude mcp list in your terminal. You can also ask the agent to invoke the ping tool to check if the service is actively responding to requests.

Run headless Ensembl queries directly from your terminal using Claude Code.

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Setup Ensembl with Claude Code

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Ensembl MCP Server terminal pipelines

You live in the terminal, and now your genomic queries do too. Claude Code connects to this MCP server and executes `get_sequence_id` straight from the command line. You can pipe the resulting sequence data directly into your local alignment tools or shell scripts. There is no GUI overhead. If a cron job needs to verify the latest REST API version, your agent runs `get_info_rest` and logs the output. It handles the raw JSON responses and formats them exactly how your pipeline expects.

Headless variant and allele fetching

Continuous integration workflows often require validating variant data against a known truth. Claude Code triggers `get_variation` to pull genotypes and population data during a build step. If it needs allele specifics, it hits `get_ga4gh_beacon`. The agent executes these fetches autonomously within your CI/CD environment. It parses the GA4GH schema using `search_ga4gh_variants` and fails the build if the expected alleles are missing, keeping your downstream databases clean.

Bulk identifier resolution

Updating ten thousand outdated identifiers by hand is a waste of time. Claude Code reads your text file and feeds chunks into `get_lookup_bulk`. It maps the species and database for multiple identifiers in seconds. For identifiers that have been deprecated, the agent falls back to `get_archive_id` to find the latest version. It then rewrites your input file with the updated stable IDs, fully automating the data scrubbing process.

Setup guide

Set up Ensembl MCP in Claude Code

Prerequisites

Claude Code CLI installed (npm install -g @anthropic-ai/claude-code)
Active Vinkius subscription with a valid endpoint token

1

Run the add command

Open your terminal and run the command shown on the right. Replace [YOUR_TOKEN_HERE] with your endpoint token from cloud.vinkius.com. Use --scope user to make it available across all projects.
2

Verify the connection

Start a Claude Code session and type /mcp to list connected servers. You should see ensembl-mcp with a green status indicator.
3

Start using tools

Ask Claude Code something like "Check my latest Ensembl transactions." It will automatically discover and invoke the available Ensembl tools.

Terminal

claude mcp add --transport http ensembl-mcp https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp

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Prerequisites

Claude Code CLI installed
Active Vinkius subscription with a valid endpoint token

1

Open the config file

Create or edit .mcp.json in your project root for project-level scope, or ~/.claude.json for user-level scope.
2

Add the Ensembl MCP

Paste the JSON snippet shown on the right into the mcpServers object. Replace [YOUR_TOKEN_HERE] with your endpoint token from cloud.vinkius.com.
3

Restart Claude Code

Start a new Claude Code session. Type /mcp to confirm the server is connected. The tools will be automatically available in your conversation.

.mcp.json

{
  "mcpServers": {
    "ensembl-mcp": {
      "type": "url",
      "url": "https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp"
    }
  }
}

Get your connection token →

Independent Platform Disclaimer: Vinkius is an independent platform and is not affiliated with, endorsed by, sponsored by, verified by, or otherwise authorized by Ensembl. All third-party trademarks, logos, and brand names are the property of their respective owners. Their use on this website is strictly for informational purposes to identify service compatibility and interoperability.

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Common questions about Ensembl MCP in Claude Code

Run `claude mcp add --transport http ensembl-mcp -- `. Ensure all flags come before the server name. Claude Code stores this configuration in your `~/.claude.json` file.

Yes. You can ask the agent to fetch a sequence via `get_sequence_region` and output it as standard text. You then pipe that directly into tools like BLAST or grep right in your shell.

It does. If your script fails due to coordinate mismatches, the agent will run `get_map` to convert the coordinates from the old assembly to the new one, then patch your script.

Run `claude mcp list` in your terminal. You can also ask the agent to invoke the `ping` tool to check if the service is actively responding to requests.

Your terminal executes queries for homology data and cross-references via a secure, ephemeral connection. Vinkius handles the authentication routing without inspecting the payload. Your specific sequence ID targets remain completely private.

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