Data released on May 11, 2015
Many bioinformatics tools use reference data, such as genome assemblies or sequence databanks. The Galaxy web-based platform for data intensive biomedical research (http://usegalaxy.org/) offers multiple ways to give access to this data through its web interface. However, the process of adding new reference data was customarily manual and time consuming, even more so when this data needed to be indexed in a variety of formats (e.g. Blast, Bowtie, BWA, or 2bit). BioMAJ is a widely used and stable software program that is designed to automate the download and transformation of data from various sources.
To ease the process of giving access to reference data in Galaxy, the BioMAJ2Galaxy module has been developed to enable the gap between BioMAJ and Galaxy to be bridged. With this module, it is now possible to configure BioMAJ to automatically download some reference data, to then convert and/or index it in various formats, and then make this data available in a Galaxy server using data libraries or data managers. A snapshot of the code is archived here, but see the genouest GitHub for the most up-to-date version:
Bretaudeau, A., Monjeaud, C., Le Bras, Y., Legeai, F., & Collin, O. (2015). BioMAJ2Galaxy: automatic update of reference data in Galaxy using BioMAJ. GigaScience, 4(1). doi:10.1186/s13742-015-0063-8