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The 2017 Galaxy Community Conference (GCC2017) is being held in Montpellier, France, 26-30 June.  GCC2017 will include keynotes and accepted talks, poster sessions, demos, birds-of-a-feather meetups, exhibitors, and plenty of networking opportunities. There will also be three days of pre-conference activities, including hackathons and training. If you work in data-intensive biomedical research, there is no better place than GCC2017 to present your work and to learn from others.
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Friday, June 30 • 17:05 - 17:06
Using Galaxy as a platform for continuous software development

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Boris Simovski 1, Geir Kjetil Sandve 1, *, Sveinung Gundersen 1,

 1 : Department of Informatics, University of Oslo [Oslo]  (UiO), Oslo Norway
 * : Corresponding author

Galaxy is typically used as a platform for disseminating already functioning bioinformatics tools to non-programmers, often by wrapping existing libraries or command-line tools in a user-friendly web interface. In Oslo, we have for nine years used Galaxy in a markedly different setting - developing novel methodology directly in the form of Galaxy tools. We have even been running code through a Galaxy interface during the initial trial-and-error phase of correcting syntax, debugging errors and shaping functionality.Many would consider such direct development within a Galaxy interface as inconvenient. As this has nonetheless become a preferred approach for us, we believe we have evolved routines and a technical setup that represents a novel use case for the Galaxy system. Briefly, our approach brings many of the usual benefits of Galaxy in terms of tracking of executions and sharing of functionality to the setting of prototypic methodology development. Despite some previous weaknesses, we have used our approach for 21 publications on novel methodology and application of custom methodology in the form of Galaxy tools. This year we have finally updated to a modern and appropriate infrastructure, consisting of several connected git repositories, dozens of active branches and deployment based on continuous integration.We will in the talk present the advantages we get as compared to the standard approach of initially developing code locally and testing it out by execution through the command line. We will also present potential challenges and disadvantages, delineating for whom we believe such an approach may be useful.


Geir Kjetil Sandve

University of Oslo
avatar for Boris Simovski

Boris Simovski

University of Oslo
University of Oslo

Friday June 30, 2017 17:05 - 17:06
Einstein Auditorium Le Corum, Level 0

Attendees (12)