MCP server

Gdc

io.github.pipeworx-io/gdc

Checked 26 Oct 2026, 08:29 UTC · Connected to it and listed its tools

NCI Genomic Data Commons (GDC) MCP.

Website Source

At a glance

Type

MCP server

Publisher

pipeworx.io (verified by the MCP Registry)

Status

Working at last check

Tools

46

Token cost

About 27,012 tokens per request

Sets up in

Claude Code, Claude Desktop, Codex, Gemini CLI, Cursor, VS Code, Antigravity, ChatGPT, OpenAI API, Grok

Last checked

26 Oct 2026, 08:29 UTC

Connect it to your agent

Add to CursorAdd to VS CodeVS Code Insiders

Opens the app, which shows the server and asks you to confirm. For other apps, copy the setup below.

Claude Code

claude mcp add --transport http gdc https://gateway.pipeworx.io/gdc/mcp

Claude Desktop

Settings → Connectors → Add custom connector, and paste the URL.

Codex (config.toml)

[mcp_servers.gdc]
url = "https://gateway.pipeworx.io/gdc/mcp"

Gemini CLI

{"mcpServers":{"gdc":{"httpUrl":"https://gateway.pipeworx.io/gdc/mcp"}}}

Cursor

{"mcpServers":{"gdc":{"url":"https://gateway.pipeworx.io/gdc/mcp"}}}

VS Code

{"servers":{"gdc":{"type":"http","url":"https://gateway.pipeworx.io/gdc/mcp"}}}

Antigravity

agy mcp add gdc https://gateway.pipeworx.io/gdc/mcp

ChatGPT

Settings → Apps & Connectors → Advanced settings: turn on Developer mode, then Create a connector and paste the URL. Which plans can do this varies.

OpenAI API (Responses tools)

{"type":"mcp","server_label":"gdc","server_url":"https://gateway.pipeworx.io/gdc/mcp","require_approval":"always"}

Grok (xAI API tools)

{"type":"mcp","server_label":"gdc","server_url":"https://gateway.pipeworx.io/gdc/mcp"}

Tools

• get_project ~127 tokens
  Look up a single NCI GDC project by project_id (e.g. "TCGA-BRCA") and get its details plus summary counts (case_count, file_count). Keyless, open-access metadata.
• list_projects ~152 tokens
  List NCI Genomic Data Commons cancer-genomics projects (TCGA, TARGET, CPTAC, etc.), ranked by case count. Returns project_id, name, program, primary site(s) and disease type(s). Keyless, open-access metadata.
• search_cases ~192 tokens
  Search NCI GDC cancer cases (patients/samples) by primary site and/or project. Returns case_id, submitter_id, primary site, disease type and project_id. Keyless, open-access metadata.
• search_files ~238 tokens
  Search NCI GDC genomic data files by project and/or data category (e.g. "Transcriptome Profiling", "Simple Nucleotide Variation", "DNA Methylation"). Returns file_id, file_name, data category/type/format, access level and file size. Keyless, open-access metadata.

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