Galaxy Help

Galaxy is a popular platform used in bioinformatics for running various data analyses, including genome assembly, mapping, and more. This guide will help you get started with Galaxy and provide an overview of its key features and functions.

1 Accessing Galaxy

To start using Galaxy, visit the following URL:

2 Creating an Account

If you don’t already have an account, you’ll need to create one:

  1. Click on the Authentification et Enregistrement (Login/Register**) button in the upper bar.
  2. Select Don’t have an account? Register here and fill out the form with your details.

Once your account is created, you can log in and save your workflows and analyses.

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3 Getting More Resources (Only Available During Practical Sessions)

To ensure you have sufficient resources for your practical sessions, follow these steps:

  1. Make sure to use the French version of Galaxy.
  2. During the practical sessions, additional resources will be reserved for you. Go to the following URL to join the training session:
  3. After joining, you can return to Galaxy and continue working with the reserved resources.

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You can then return to galaxy.

4 Uploading Data

To upload your sequencing data or other files:

  1. Click on the Upload Data button located on the top left of the page under the Tools section.

  2. A panel will appear where you can drag-and-drop files or choose them from your computer.

Make sure that your data is correctly formatted and meets the requirements for the specific tools you’ll be using.

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5 Running Tools and Workflows

Galaxy offers many bioinformatics tools, each designed to perform specific tasks like quality control, mapping, assembly, and annotation. To use these tools effectively:

  1. Explore the Tools section on the left panel.
  2. When you select a tool, Galaxy will display options for configuring it. Follow the tool documentation to understand which parameters need adjustment based on your data.
  3. Many tools allow for custom inputs, but default settings often work well for general cases.

Make sure to familiarize yourself with the help sections of each tool, as they provide detailed descriptions and usage tips.

Your job will be queued, and you can monitor its progress in the History panel on the right-hand side of the screen.

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6 Understanding Job Status in the History Panel

  • Green: The job has successfully completed.
  • Red: The job failed. You can click on the red dataset to see the error log.
  • Yellow: The job is still running.
  • Gray: The job is queued and waiting to be processed.

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7 Viewing and Downloading Results

Once your job is completed, ithe results appear in the History panel. You can:

  • Click on the dataset to view the output directly in Galaxy.
  • Download the results by clicking on the download icon next to the dataset in the History panel.

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8 Help and Troubleshooting

If you encounter any issues, Galaxy has extensive documentation and community support:

These resources provide guides for using Galaxy, troubleshooting tips, and examples of common workflows.

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By following these steps, you should be able to navigate Galaxy efficiently and complete your analyses. As you progress, feel free to add your own notes, screenshots, and comments to enhance your understanding of the platform.