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GCC 2017 has ended
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.

The full printed program is also available.
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Wednesday, June 28 • 12:30 - 15:00
Conda and Containers for Tool Dependencies - A Developers Perspective

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Conda Slides, Container Slides

This workshop is aimed at people with some experience developing tools but may also be of use to deployers who need to manage complex sets of dependencies for tools.

Galaxy tools define the applications and other dependencies they require to run using their requirements section. This training session will cover the elements of the requirements section and how Galaxy can be configured to utilize these.

The current best practice for resolving these dependencies is using Conda and Bioconda, and so a substantial amount of time will be spent on these topics. We will go through the process of creating, testing, and publishing a Bioconda package. We will work through an example of connecting these packages to Galaxy.

We will also discuss how the Biocontainers project constructs Docker containers from Bioconda packages and how to emulate this process for local testing before publication. Finally, we will review approaches to leveraging these containers from Galaxy to run jobs within containers.

Prerequisites:
  • Basic Knowledge of Galaxy Tools, or attendance to either a basic session on building tools or deploying Galaxy.
  • A wi-fi enabled laptop with a modern web browser. Google Chrome, Firefox and Safari will work best.

Instructors
avatar for Abdulrahman Azab

Abdulrahman Azab

Senior Engineer, University of Oslo
avatar for John Chilton

John Chilton

Galaxy Project, Penn State University
avatar for Marius van den Beek

Marius van den Beek

Institut Curie, Paris
avatar for Nicola Soranzo

Nicola Soranzo

Earlham Institute


Wednesday June 28, 2017 12:30 - 15:00
Rondolet Room Level 2, Le Corum

Attendees (23)