Automatic update of reference data in Galaxy using BioMAJ.

Anthony Bretaudeau 1, 2 Yvan Le Bras 2 Cyril Monjeaud 2 Olivier Collin 2
1 SYMBIOSE - Biological systems and models, bioinformatics and sequences
IRISA - Institut de Recherche en Informatique et Systèmes Aléatoires, Inria Rennes – Bretagne Atlantique
2 Plateforme bioinformatique GenOuest [Rennes]
IRISA - Institut de Recherche en Informatique et Systèmes Aléatoires, UR1 - Université de Rennes 1, Plateforme Génomique Santé Biogenouest®, Inria Rennes – Bretagne Atlantique
Abstract : Many bioinformatic tools require the use of reference data like genome assemblies or sequence databanks. Galaxy offers multiple ways to give access to this data in its web interface: data libraries, *.loc files and more recently the introcution of data managers. However, until now, the process of adding a new reference data was essentially manual and time consuming, even more when this data need to be indexed in a variety of formats (blast, bowtie, bwa, 2bit, ...). The recent release of data managers is a first step for the automation of data download and indexing, but it still requires some manual intervention to launch the download and subsequent automatic indexing. Furthermore, it was designed with a galaxy-centric view, not taking into account that reference data are often used outside Galaxy, for example using command line or concurrent systems like Mobyle. BioMAJ is a widely used and stable software designed to automate the download and transformation of data from various sources. This data can be used directly from the command line, or in more complex systems like Mobyle, or using a REST API. We have developed BioMAJ post-processes to automatically populate the Galaxy data libraries or data managers, avoiding data and transformation duplications. In this talk we will make a brief overview of the difference way to manage reference data in Galaxy. We will then present the solution that was developed to fill the gap between BioMAJ and Galaxy. We will then present some considerations in regard to security aspects when a reference data needs to be available only to a group of users. Finally on-going developments and ideas will be evoked.
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Conference papers
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https://hal.inria.fr/hal-01102421
Contributor : Anthony Bretaudeau <>
Submitted on : Monday, January 12, 2015 - 4:55:14 PM
Last modification on : Friday, November 16, 2018 - 1:31:10 AM

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  • HAL Id : hal-01102421, version 1

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Anthony Bretaudeau, Yvan Le Bras, Cyril Monjeaud, Olivier Collin. Automatic update of reference data in Galaxy using BioMAJ.. Galaxy Day 2014, Institut Français de Bioinformatique, Dec 2014, Paris, France. ⟨hal-01102421⟩

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