isabl

🧬🤖 Isabl MCP Server

Talk to your genomics data. MCP server + knowledge base for the Isabl platform.

Install

Claude Code

/plugin marketplace add juanesarango/isabl-mcp
/plugin install isabl

Installs the MCP server (11 tools) + 8 guided skills as /isabl-* slash commands (type /isabl to see all). Credentials are auto-discovered from ~/.isabl/settings.json. For MCP only (no skills): claude mcp add isabl -- uvx isabl-mcp.

Cursor

Click the badge above, or add to .cursor/mcp.json:

{
  "mcpServers": {
    "isabl": {
      "command": "uvx",
      "args": ["isabl-mcp"],
      "env": {
        "ISABL_API_URL": "https://your-isabl-instance.com/api/v1/",
        "ISABL_API_TOKEN": "your-token"
      }
    }
  }
}

Codex

Add to ~/.codex/config.toml:

[mcp_servers.isabl]
command = "uvx"
args = ["isabl-mcp"]
env = { "ISABL_API_URL" = "https://your-isabl-instance.com/api/v1/", "ISABL_API_TOKEN" = "your-token" }

Other MCP clients

uvx isabl-mcp        # run directly, no install needed
pip install isabl-mcp # or install globally

Works with any MCP-compatible client (Windsurf, Zed, Claude Desktop, etc.).

What's included

Component	Claude Code Plugin	MCP only (Cursor, Codex, etc.)
11 MCP tools (query, debug, search)	✅	✅
8 MCP prompts (guided workflows)	✅	✅ (client support varies)
8 skills (/isabl-* slash commands)	✅	❌ (Claude Code only)
Knowledge base (347 docs)	✅	✅
Auto-discover credentials	✅	✅

Credentials

The server auto-discovers your API URL and token from ~/.isabl/settings.json (created by isabl_cli login). No env vars needed if you've already logged in.

You can also set them explicitly:

export ISABL_API_URL="https://your-isabl-instance.com/api/v1/"
export ISABL_API_TOKEN="your-token"

Env vars always take precedence over the settings file.

What can I ask?

"Show me all failed analyses in project 102"

"How many WGS experiments do we have for patient ISB_H000001?"

"Analysis 12345 failed. Show me the error logs and help me figure out what went wrong"

"Get the VCF file paths from all succeeded MUTECT analyses in project 102"

"How do I write a new paired tumor-normal application?"

"Give me a summary of project 102"

Tools (11)

Tool	Description
isabl_query	Query any API endpoint with Django-style filters
isabl_get_tree	Get Individual → Sample → Experiment → Analysis hierarchy
isabl_get_results	Get result file paths from a completed analysis
isabl_get_logs	Read stdout/stderr/script logs from any analysis
get_apps	Search for installed applications by name
get_app_template	Generate boilerplate code for a new application
merge_results	Collect and preview result files across multiple analyses
project_summary	Get project stats: experiment counts, analysis breakdown
search_knowledge	Search 347 docs from Isabl's code, docs, and API specs
get_knowledge_tree	Browse the hierarchical knowledge tree
get_knowledge_doc	Get full content of any knowledge base document

Skills (8) — Claude Code only

Skills are guided multi-step workflows available as /isabl-* slash commands. Included automatically with the plugin install.

Skill	Purpose
/isabl-query-data	Query data from Isabl API
/isabl-write-app	Create a new Isabl application
/isabl-monitor-analyses	Track analysis status
/isabl-debug-analysis	Debug a failed analysis
/isabl-merge-results	Aggregate results across analyses
/isabl-submit-data	Submit new sequencing data
/isabl-project-report	Generate project status reports
/isabl-run-pipeline	Run multiple apps as pipeline

How it works

You (plain English) → AI Assistant → MCP Server → Isabl API → Your data
                                  |
                                  └→ Knowledge Base → Platform docs & code