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📖 BioFinder MCP — Reference

Complete reference for the CLI commands, MCP tools, and MCP resources.

CLI commands

biofinder_client.py <command> [args]
Command Arguments Description
find <name> Tool name (string) Look up a tool by name
search <query> Query string Search by function or description
versions <name> Tool name (string) List all container versions for a tool
list [n] Optional integer (default 50) Browse available tools
interactive — Start interactive REPL

find

./biofinder_client.py find fastqc
./biofinder_client.py find "bwa-mem2"
  • Case-insensitive.
  • Tries id, name, biotools, and biocontainers fields from metadata.
  • Falls back to substring matching if no exact match.
  • Handles hyphen/underscore variants automatically.

search

./biofinder_client.py search "quality control"
./biofinder_client.py search variant calling       # quotes optional for multi-word
  • Scores all metadata records against your query.
  • Returns results ranked by relevance score (highest first).

versions

./biofinder_client.py versions samtools
  • Returns all versions sorted newest-first.
  • Each entry includes CVMFS path, size in MB, and last-modified date.

list

./biofinder_client.py list
./biofinder_client.py list 200
  • Alphabetical, columnar output.
  • Draws from both the metadata catalog and the container index, so includes tools that have containers but no metadata.

interactive

./biofinder_client.py interactive

Starts a REPL. Available commands inside interactive mode:

find <tool_name>
search <description>
versions <tool_name>
list [limit]
help
quit / exit

MCP tool schema

The server implements the Model Context Protocol and can be used by any MCP-compatible client (LLMs, workflow tools, etc.).

find_tool

{
  "name": "find_tool",
  "inputSchema": {
    "type": "object",
    "properties": {
      "tool_name": { "type": "string" }
    },
    "required": ["tool_name"]
  }
}

Returns: Formatted text containing tool metadata, latest container path, copy-pastable usage examples, and a summary of other available versions.

search_by_function

{
  "name": "search_by_function",
  "inputSchema": {
    "type": "object",
    "properties": {
      "description": { "type": "string" },
      "limit":       { "type": "integer", "default": 3 }
    },
    "required": ["description"]
  }
}

Returns: Formatted text with a ranked list of matching tools, each with description, operations, latest container tag, and a quick-start command.

get_container_versions

{
  "name": "get_container_versions",
  "inputSchema": {
    "type": "object",
    "properties": {
      "tool_name": { "type": "string" }
    },
    "required": ["tool_name"]
  }
}

Returns: Formatted text listing every container version for the tool, sorted newest-first. Each entry shows version tag, CVMFS path, size (MB), and last-modified date.

list_available_tools

{
  "name": "list_available_tools",
  "inputSchema": {
    "type": "object",
    "properties": {
      "limit": { "type": "integer", "default": 50 }
    },
    "required": []
  }
}

Returns: Formatted text with an alphabetical list of tool names.

MCP resources

Resources are read via read_resource(uri).

URI MIME type Content
biocontainer://cache-info application/json generated_at, cvmfs_root, entry_count
biocontainer://tool-list text/plain Newline-separated list of tool names (up to 1000)

Container tag format

Tags follow the Bioconda build convention:

<version>--<build_string>

Examples:
  0.12.1--hdfd78af_0      # version 0.12.1, build hash hdfd78af, build number 0
  1.17--h00cdaf9_0        # version 1.17
  3.0.1--h503566f_0       # version 3.0.1

When multiple containers exist for the same version (different build strings), BioFinder sorts by the full tag string as a tiebreaker, so the "latest" shown may not always be the numerically last build. Use versions to inspect all options.

CVMFS path format

All container paths follow this pattern:

/cvmfs/singularity.galaxyproject.org/all/<tool_name>:<tag>

Paths are valid when the CVMFS filesystem is mounted at /cvmfs/singularity.galaxyproject.org. On systems without CVMFS, the paths will not resolve — BioFinder does not validate path existence at query time.