Quick Start Guide: mcp-manager and jira-helper

July 11, 2026 · View on GitHub

This guide provides a streamlined set of instructions for developers to get up and running with the mcp-manager tool and the jira-helper MCP server.

1. Prerequisites

Python 3.11+
uv (for installing mcp-manager and managing per-server environments)

If you don't have uv, install it with:

curl -LsSf https://astral.sh/uv/install.sh | sh
uv tool update-shell   # ensure uv's tool bin dir is on your PATH

2. Install `mcp-manager`

Install the mcp-manager CLI tool globally with uv:

# Install from this checkout
uv tool install ./utils/mcp_manager

# Or install from GitHub
uv tool install "git+https://github.com/dawsonlp/BaseMcpServer.git#subdirectory=utils/mcp_manager"

Verify the installation:

mcp-manager --version
mcp-manager --help

Note: mcpmanager (without the hyphen) is registered as an alias.

3. Install the `jira-helper` Server

Use mcp-manager to install the jira-helper server in an isolated environment:

mcp-manager install jira-helper --source servers/jira-helper --force

--source: Points to the directory containing the server's source code.
--force: Overwrites any existing server with the same name.

The server will be installed under ~/.config/mcp-manager/servers/jira-helper/.

4. Configure for Multiple Jira Instances

The jira-helper server is configured via a config.yaml file where you add connection details for each Jira instance.

Navigate to the jira-helper configuration directory:
```
cd ~/.config/mcp-manager/servers/jira-helper
```
Create the configuration file: Copy the example configuration to create your own:
```
cp config.yaml.example config.yaml
```

Edit the configuration file: Open config.yaml and configure your Jira instances:

Example config.yaml:

# ~/.config/mcp-manager/servers/jira-helper/config.yaml

# Optional: which instance to use when a tool call doesn't specify one.
# If omitted, the first defined instance is used as the default.
default_jira_instance: personal

instances:
  personal:
    description: Personal Jira Instance
    jira:
      url: https://your-personal-space.atlassian.net
      username: your-email@example.com
      api_token: YOUR_JIRA_API_TOKEN
    # Confluence is optional — include only if you want Confluence tools too.
    confluence:
      url: https://your-personal-space.atlassian.net
      username: your-email@example.com
      api_token: YOUR_JIRA_API_TOKEN

  work:
    description: Work Jira Instance
    jira:
      url: https://your-company.atlassian.net
      username: your-work-email@example.com
      api_token: YOUR_OTHER_JIRA_API_TOKEN

Getting Jira API Tokens:

Go to your Atlassian Account Settings
Navigate to Security → API Tokens
Create a new token for each instance
Replace the placeholder values with your actual URLs, emails, and tokens

5. Configure Cline Integration

Configure VS Code Cline to use the jira-helper server:

mcp-manager sync --platform cline

This automatically updates your VS Code settings to include the jira-helper server.

6. Verify Your Setup

Check your complete MCP system status:

mcp-manager info tree

This command displays:

System information (Python version, total servers, disk usage)
Platform integration status (VS Code Cline, Claude Desktop)
Server counts by platform

You should see jira-helper counted in the VS Code Cline servers, and both platforms showing "Available" status.

7. Using Multiple Jira Instances

When using Jira tools in your editor, you can specify which instance to use:

Default instance: Commands use your configured default_jira_instance
Specific instance: Use the instance_name parameter in tool calls

Example Usage:

list_jira_projects with instance personal
get_issue_details for issue PROJ-123 on work instance
create_jira_ticket on your default instance

Troubleshooting

If you encounter issues:

List installed servers: mcp-manager list
Check config paths: mcp-manager show jira-helper
Validate the install: mcp-manager validate jira-helper
Run the server directly (stdio): ~/.config/mcp-manager/servers/jira-helper/.venv/bin/jira-helper stdio
Verify Jira credentials: check your API tokens and URLs
Restart VS Code after configuration changes

You are now ready to use the jira-helper with all your configured Jira instances directly from your editor!