BioBeamerLauncher

BioBeamerLauncher is a cross-platform launcher for BioBeamer. It fetches a configuration file from a public git repository, determines the correct BioBeamer version to use, and runs BioBeamer with the specified configuration.

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Quick Start (Recommended for Most Users)

1. Download and Extract

• Download the release package (zip or tar.gz) for your platform.
• Extract it to a folder of your choice.

2. Install (One-Time Setup)

• Windows: Double-click or run setup.bat.
• Linux/macOS: Run bash setup.sh in a terminal.

This will: - Set up a Python environment using the included uv tool - Download and install the BioBeamer Launcher from GitHub

3. Start the Launcher

• Windows: Double-click or run start.bat.
• Linux/macOS: Run bash start.sh in a terminal.

This will: - Activate the environment - Start the BioBeamer Launcher using the default configuration (config/launcher.ini)

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Requirements

• Git must be installed and available in your system PATH.
• Internet access is required to fetch configuration files and repositories.
• No need to pre-install Python or pip; the setup script will handle this automatically using uv.
• robocopy (Windows) and/or scp/ssh (Linux/Unix) must be installed and available in your system PATH for file transfer operations and integration tests.
• If you want to use scp for remote transfers, you must set up passwordless SSH access (e.g., using SSH keys) to the remote host in advance. The target path in the XML config must be in the format host:/path (or user@host:/path if a username is needed).

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Updating

To update to the latest version, simply re-run setup.bat or setup.sh.

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Troubleshooting

• The first run may take a few minutes as dependencies are downloaded.
• Make sure you have an internet connection for the initial setup.
• If you encounter issues, check the log files in the log/ directory.
• For advanced users, you can activate the environment manually:
  • Windows: call biobeamer-launcher-venv\Scripts\activate.bat
  • Linux/macOS: source biobeamer-launcher-venv/bin/activate
• If you need to use a different configuration file, edit start.sh or start.bat and change the path after --config.

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Debugging

If you encounter issues or need to debug BioBeamer problems:

Quick Debug Setup

```bash

Get debug information with setup

python -m biobeamer_launcher.launcher --config config/launcher.ini --debug ```

This command will: - ✅ Set up the exact BioBeamer environment used in production - ✅ Print copy-paste ready debugging commands
- ✅ Show IDE configuration paths - ✅ Provide step-by-step debugging instructions

For detailed debugging instructions, see DEBUGGING.md

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Developer & Advanced Usage

Manual Installation

If you want to install the launcher and its dependencies manually (e.g., for development):

sh pip install .

To install with optional test dependencies (for running tests):

sh pip install .[test]

Testing

To run the test suite, make sure you have installed the test dependencies as above, then run:

sh pytest

Or, to run a specific test file:

sh pytest tests/test_launcher_real_integration.py

You can also use unittest if you have tests written for it:

sh python -m unittest discover

Directory Structure

• pyproject.toml — Project metadata and dependencies
• src/biobeamer_launcher/launcher.py — Main launcher script

Usage (Development)

1. Clone this repository: sh git clone https://github.com/fgcz/BioBeamerLauncher.git cd BioBeamerLauncher
2. Run the launcher: sh python src/biobeamer_launcher/launcher.py

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Workflow

1. User runs the launcher
2. Launcher fetches config from git
3. Launcher ensures correct BioBeamer version is present
4. Launcher runs BioBeamer

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For more details, see the source code and comments in src/biobeamer_launcher/launcher.py.

License

See LICENSE file for details.