Overview

This guide will help you install a local deployment of the Galaxy fluxomics workflow developed by the MetaboHUB-MetaToul-FluxoMet & MetaSys teams from the Toulouse Biotechnology Institute. It is intended for development and maintenance purposes.

Prerequisites

• Working knowledge of Git, Bash, and the Galaxy workflow manager
• Python 3 installed on your system (see python.org for installation instructions)
• A Linux system (fully fledged or Virtual Machine)
  • Note: The Galaxy instance is designed to run on Linux machines. It will not work on Windows and has not been tested on macOS.

Project Structure

This project is built on several separate Python tools. Git submodules are used to facilitate easy switching between workflow-level development and specific tool development. For more information on Git submodules, see:

• Git Tools - Submodules
• Working with Submodules

Getting Started

Clone the Repository

git clone https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m.git
cd tools_w4m

Repository Structure

The repository contains the following directories:

• galaxy: A Git submodule linked to the main Galaxy repository (currently linked to the 25.0 release). The commit number references the downloaded submodule version.
• packages: Contains submodules for each individual tool in the workflow, as well as scripts for updating submodules and installing tools into the Galaxy virtual environment.
• test-data: Contains test data for the workflow.
• tool_wrappers: Contains XML files for configuring tool execution and GUI display.

Install Tool Packages

Run the installation script to download the latest versions of the workflow tools and install them into the Galaxy virtual environment:

cd packages
sh ./install_packages.sh

This will install the different software into the Galaxy .venv, which can be found at ./galaxy/.venv/.

Install the Wrappers and Make the Tools Visible to Galaxy

The next step is to ensure Galaxy has access to the tool XML wrappers. This can be done by following the steps found here. The actual tool code does not need to be copied into the tools directory as it is already installed within the Galaxy venv. The most important step is to make Galaxy aware of the tools by adding them to the tool_conf.xml file.

Run Galaxy

You can now launch the Galaxy instance with:

sh ./galaxy/run.sh

Note: Galaxy will be accessible at http://localhost:8080 by default once the server has started.

Next Steps

After launching Galaxy, you can:

• Access the Galaxy interface through your web browser
• Test the workflow tools with the provided test data
• Configure additional settings as needed for your development environment

Troubleshooting

Common Issues

• Port Already in Use: If port 8080 is already occupied, you can specify a different port by modifying the Galaxy configuration file or using the --port flag.
• Permission Errors: Ensure you have the necessary permissions to execute scripts and access the Galaxy directory.
• Missing Dependencies: If you encounter errors related to missing Python packages, verify that the installation script completed successfully and that all submodules were properly initialized.

Additional Resources

• Galaxy Project Documentation
• MetaboHUB Website
• Workflow Repository

Contributing

For contributions or issues, please refer to the project's GitHub repository and follow the standard pull request workflow.

License

Please refer to the LICENSE file in the repository for licensing information.