foundry-connect

foundry-connect connects Foundry Connect — the bioinformatics pipeline platform — to Claude. It ships a Claude Code plugin (the foundry-pipelines skill plus /foundry-run, /foundry-status, /foundry-results commands) and per-surface connect guides for the web/desktop apps, all built on Foundry Connect's remote MCP server. Once connected, you can explore runs, pull result files, analyze data in chat, share results back, and duplicate/launch pipeline runs — conversationally, from whichever Claude surface you use.

Surface → path

Surface	How you connect
Claude Code (CLI)	plugin, via this marketplace — see connect/claude-code.md
Claude Code in VS Code	same plugin (needs VS Code extension ≥ v2.1.203 for remote MCP) — see connect/claude-code.md
claude.ai / Claude for Science	MCP custom connector — see connect/claude-ai.md
Claude Desktop	MCP connector (or a .mcpb bundle, if your instance provides one) — see connect/claude-desktop.md

Quickstart (~90 seconds, Claude Code)

1. Start a Claude Code session, then type these slash commands at the prompt (not in your terminal):

   /plugin marketplace add UMMS-Biocore/foundry-connect-plugin
   /plugin install foundry-connect@foundry-connect
   

2. When prompted, enter your Foundry Connect instance URL — the base URL only, e.g. https://foundry.your-org.edu. No trailing slash, and no /mcp on the end: the plugin appends /mcp itself, so pasting the connector URL from Profile → Connect to Claude (which already ends in /mcp) produces .../mcp/mcp and fails silently.

3. Restart your Claude Code session. Plugin-provided MCP servers load at session start, so the plugin you just installed isn't connected until you exit and run claude again. Skipping this is the most common reason the plugin looks installed but Foundry Connect never appears.

4. Run /mcp — you should see a server named foundry, connected. If it shows viafoundry instead, that's an older manual claude mcp add connection rather than this plugin; both work, but remove the old one with claude mcp remove viafoundry so you don't end up with two servers exposing the same tools.

5. First tool call opens a browser to sign in to Foundry Connect (OAuth) — no token to copy.

6. Ask Claude: "show my last 5 runs".

7. Try your first run: /foundry-run — it duplicates an existing run, lets you edit inputs, and launches it, confirming with you before anything is written or executed.

For claude.ai, Claude for Science, or Claude Desktop, see the connect guide for your surface in connect/ — those connect Foundry Connect as an MCP connector rather than a plugin.

Docs

• connect/claude-code.md — Claude Code CLI + VS Code
• connect/claude-ai.md — claude.ai / Claude for Science
• connect/claude-desktop.md — Claude Desktop
• Your Foundry Connect instance's docs (Developer Guides → API Guide → MCP Integration) cover Personal Access Tokens and manual client configuration if you need them.

Safety

Read/inspect actions (listing runs, downloading or loading files, fetching reports) run freely. Anything that writes or executes — creating a dataset, uploading a file, duplicating a process, launching a run or app — requires your explicit "yes" to a plain-language summary before Claude calls it. Nothing is written or run without asking first.

License

Apache-2.0 — see LICENSE.