Expanding the Galaxy's reference data

Area of Science:

• Bioinformatics
• Computational Biology
• Data Management

Background:

• Managing reference datasets is crucial for bioinformatics analyses.
• Refgenie provides a system for organizing, retrieving, and sharing reference datasets.
• Galaxy is a widely used platform for bioinformatics workflows.

Purpose of the Study:

• To describe the integration of the refgenie reference asset management system into the Galaxy platform.
• To enhance the management and accessibility of reference datasets within Galaxy.
• To provide users with easier access to essential bioinformatics resources.

Main Methods:

• Integration of refgenie into the core Galaxy framework (version 22.01).
• Development of a Galaxy Data Manager tool for graphical interface to refgenie's retrieval functionality.
• Utilizing CVMFS (CernVM File System) for a distributed repository of reference datasets.

Main Results:

• Galaxy can now utilize reference datasets managed by refgenie.
• A user-friendly Data Manager tool facilitates remote reference data retrieval.
• Extensive reference datasets are accessible via CVMFS mirrors globally, usable both within and outside Galaxy.

Conclusions:

• The integration of refgenie significantly improves reference data management in Galaxy.
• This enhancement streamlines bioinformatics workflows by simplifying data access.
• The combined system offers a robust solution for managing and utilizing critical bioinformatics resources.