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Glama
GBA-BI
by GBA-BI

Server Configuration

Describes the environment variables required to run the server.

NameRequiredDescriptionDefault
PYTHONPATHYesPath to the bioos-mcp-server/src directory
MIRACLE_ACCESS_KEYYesYour Miracle Cloud access key
MIRACLE_SECRET_KEYYesYour Miracle Cloud secret key

Instructions

Guidance the server publishes about itself, which clients place ahead of the tool catalog so the model reads it before choosing anything.

This server publishes no instructions, or was last inspected before Glama recorded them.

Capabilities

Features and capabilities supported by this server

Protocol revision2025-11-25

CapabilityDetails
tools
{
  "listChanged": false
}
prompts
{
  "listChanged": false
}
resources
{
  "subscribe": false,
  "listChanged": false
}
experimental
{}

Tools

Functions exposed to the LLM to take actions

NameDescription
validate_wdlB

验证 WDL 文件的语法正确性

list_workspaceC

列出当前登录环境的工作空间名称与描述

import_workflowC

该工具用于将 WDL 工作流上传到 Bio‑OS,支持上传单个文件或整个目录。

generate_inputs_json_template_bioosC

Bio-OS 上已导入 workflow 的 inputs.json 查询,并生成符合的输入参数模板

compose_input_jsonC

根据用户给的数值生成input.json

validate_workflow_input_jsonC

验证工作流输入 JSON 文件

submit_workflowC

提交并监控 Bio-OS 工作流

check_workflow_run_statusC

查询工作流运行状态

check_workflow_import_statusC

查询工作流导入状态

get_workflow_logsD

获取工作流执行日志

delete_submissionC

Bio-OS 删除工作流提交

create_workspace_bioosC

Bio-OS 创建新工作空间

export_bioos_workspaceD

Bio-OS 导出工作空间元信息

create_iesappC

在指定的workspace中新建一个 IES 实例,用户可在该 IES 实例上进行分析

check_ies_statusC

查看指定workspace中的指定IES 实例的创建状态

get_ies_eventsB

查看指定workspace中的指定IES实例的创建日志

upload_dashboard_fileB

上传__dashboard__.md文件到指定工作空间的S3桶

search_dockstoreD

在Dockstore中检索工作流

fetch_wdl_from_dockstoreC

从Dockstore下载工作流

get_docker_image_urlC

获取 Docker 镜像的完整 URL

build_docker_imageD

构建 Docker 镜像

check_build_statusB

检查 Docker 镜像构建状态

Prompts

Interactive templates invoked by user choice

NameDescription

No prompts

Resources

Contextual data attached and managed by the client

NameDescription

No resources

TDQS

C2.7/5.0

Scored across 22 tools

Disambiguation4/5

Most tools have distinct purposes, but there is some overlap between 'check_workflow_import_status' and 'check_workflow_run_status' which could cause confusion in monitoring workflows. Additionally, 'compose_input_json' and 'generate_inputs_json_template_bioos' both handle input JSON generation, though their descriptions suggest different contexts (user-provided values vs. template generation). Overall, the tools are well-differentiated, but a few pairs require careful reading to avoid misselection.

Naming Consistency3/5

The naming follows a mostly consistent verb_noun pattern (e.g., 'build_docker_image', 'create_workspace_bioos'), but there are deviations such as 'fetch_wdl_from_dockstore' (verb_noun_preposition) and mixed use of underscores with terms like 'Bio-OS' in names (e.g., 'export_bioos_workspace'). While readable, the lack of a strict convention across all tools reduces predictability.

Tool Count4/5

With 22 tools, the count is on the higher side but reasonable for a comprehensive bioinformatics platform covering Docker builds, workspace management, workflow handling, and IES instances. It feels slightly heavy but not excessive, as each tool appears to serve a specific function in the domain without obvious redundancy.

Completeness5/5

The tool set provides complete coverage for the bioinformatics domain, including CRUD operations for workspaces and IES instances, workflow lifecycle management (import, validate, submit, monitor, delete), and supporting utilities like Docker image handling and input generation. No significant gaps are apparent; agents can perform end-to-end tasks without dead ends.

Maintenance

ActivityInactive
ResponsivenessNo issues