BioMAJ2Galaxy: automatic update of reference data in Galaxy using BioMAJ.
Anthony Bretaudeau1, Cyril Monjeaud2, Yvan Le Bras2
1INRA, UMR Institut de Génétique, Environnement et Protection des Plantes (IGEPP), BioInformatics Platform for Agroecosystems Arthropods (BIPAA), Campus Beaulieu, Rennes, 35042 France ; INRIA, IRISA, GenOuest Core Facility, Campus de Beaulieu, Rennes, 35042 France.
Gigascience
|May 12, 2015
Summary
BioMAJ2Galaxy automates the integration of reference data into Galaxy, streamlining bioinformatics workflows. This module simplifies data management, saving time and disk space for researchers.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Bioinformatics tools rely on reference data like genome assemblies.
- Galaxy provides web access to this data, but manual addition is time-consuming.
- Indexing data in multiple formats (Blast, Bowtie, BWA, 2bit) further complicates manual processes.
Purpose of the Study:
- To automate the download, transformation, and indexing of reference data for Galaxy.
- To bridge the gap between BioMAJ and Galaxy for efficient data management.
- To provide a reliable and diskspace-saving solution for integrating reference data.
Main Methods:
- Developed the BioMAJ2Galaxy module.
- Configured BioMAJ for automatic data download and conversion.
- Integrated data into Galaxy using data libraries and data managers.
Main Results:
- BioMAJ can now automatically download, convert, and index reference data.
- The BioMAJ2Galaxy module makes data available in Galaxy servers.
- The process is automated, reliable, and saves disk space.
Conclusions:
- The BioMAJ2Galaxy module enables automatic, reliable, and diskspace-saving integration of reference data in Galaxy.
- This facilitates easier access to essential bioinformatics resources.
- The code is publicly available on GitHub.
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