Bio-OS MCP Server
by GBA-BI
Bio-OS MCP Server is a Model Context Protocol (MCP) based tool and prompt server for Bio-OS. It provides workflow management and Docker image building capabilities.
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What is Bio-OS MCP Server?
Bio-OS MCP Server is a tool designed to manage workflows and build Docker images within the Bio-OS ecosystem, leveraging the Model Context Protocol (MCP). It allows users to interact with Bio-OS functionalities through a standardized interface, streamlining development and deployment processes.
How to use Bio-OS MCP Server?
The Bio-OS MCP Server can be used either through a local installation with VSCode and the CLINE extension or via a pre-configured Docker image in Miracle Cloud. Configuration involves setting up the server path in CLINE's MCP settings and copying the contents of bioos-mcp-prompt.md into CLINE's Custom Instructions. The server provides API tools and prompts for workflow submission, validation, and Docker image building.
Key features of Bio-OS MCP Server
Workflow Management (submit, monitor, upload, validate)
Docker Image Management (build, check status, monitor progress, retrieve logs)
WDL Script Validation
Input File Template Generation
Use cases of Bio-OS MCP Server
Developing and deploying bioinformatics workflows on Bio-OS.
Building and managing custom Docker images for bioinformatics applications.
Validating WDL scripts before workflow submission.
Generating input file templates for WDL workflows.
FAQ from Bio-OS MCP Server
What is MCP?
What is MCP?
Model Context Protocol (MCP) is a standardized interface for interacting with tools and services.
How do I install the Bio-OS MCP Server?
How do I install the Bio-OS MCP Server?
You can install it locally using the provided instructions or use the pre-configured Docker image in Miracle Cloud.
What is CLINE?
What is CLINE?
CLINE is a VSCode extension recommended for interacting with the Bio-OS MCP Server.
Are prompts supported in CLINE?
Are prompts supported in CLINE?
No, prompts are currently not supported in CLINE. You need to copy the prompt contents into CLINE's Custom Instructions.
Where can I find the bioos-mcp-prompt.md file?
Where can I find the bioos-mcp-prompt.md file?
The bioos-mcp-prompt.md file should be located in the cloned Bio-OS MCP Server repository.