Loading…
GCC BOSC 2018
Attending this event?
The 2018 Galaxy Community Conference (GCC2018) and Bioinformatics Open Source Conference 2018 (BOSC2018) are joining together for a unified event to be held in Portland, Oregon, United States, June 25-30, 2018.  The event features two days of training, a two day meeting, and finish with two or four days of intense collaboration at the GCC OBF CollaborationFest Core and Encore events.  The meeting will feature joint and parallel sessions, and shared keynotes, poster and demo sessions, and social events.  Colocating GCC and BOSC will bring together the widest possible community of bioinformatics developers and practitioners into a single place.  At this event the whole will be greater than the sum of the parts.

The event is organized by Oregon Health & Science University and will be held at Reed College, a small liberal arts college in Portland. Conference housing is available in two Reed College residence hall complexesPortland is a vibrant city in the American Northwest, close to the Cascade Mountains, the Oregon Coast, and the Columbia River. 

View analytic
Tuesday, June 26 • 9:00am - 11:30am
Conda and Containers

Sign up or log in to save this to your schedule and see who's attending!

Key:  -  |  -  | IP | TD |  -  | CL

This workshop is aimed at people with some desire to develop dependencies for tools (either Galaxy or Common Workflow Language (CWL) tools).

We believe the best practice for declaring dependencies for either Galaxy or the CWL is using Conda and Bioconda. Conda is a cross platform package manager that has minimal requirements to use which makes it ideal for HPC. It can also build isolated environments ideal for platforms like Galaxy or CWL implementations. The Bioconda project is a set of Conda recipes for bioinformatics. The BioContainers project builds best practice containers automatically for all Bioconda recipes, so building a BioConda recipe for a package allows the same binaries to be used by both Galaxy (inside or outside a container) and by any conformant CWL implementation.

We will go through the process of creating, testing, and publishing a Bioconda package and we will work through an example of connecting these packages to a real world tool. Participants will be able to work through the examples using either Galaxy or CWL tools.

Prerequisites

  • Some knowledge of tool development - either CWL or Galaxy.
  • Knowledge and comfort with the Unix/Linux command line interface and a text editor. If you don't know what cd, mv, rm, mkdir, chmod, grep and so on can do then you will struggle in these workshops

Speakers
avatar for John Chilton

John Chilton

Galaxy Project, Penn State University
Galaxy Project, Penn State Universtiy


Tuesday June 26, 2018 9:00am - 11:30am
Training Venue 1