GCC BOSC 2018 has ended
The 2018 Galaxy Community Conference (GCC2018) and Bioinformatics Open Source Conference 2018 (BOSC2018) are meeting together in Portland, Oregon, United States, June 25-30, 2018.  There will be two days of training, a two+ day meeting, and four days of intense collaboration.  The meeting features joint & parallel sessions, shared keynotes, poster & demo sessions, birds-of-a-feather, and social events.  GCCBOSC is organized by Oregon Health & Science University and will be at Reed College.

Back To Schedule
Tuesday, June 26 • 9:00am - 11:30am
Conda and Containers

Sign up or log in to save this to your schedule, view media, leave feedback and see who's attending!

→ Tool Dependencies and Conda:          Slides, PDF
→ Tool Dependencies and Containers:  

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.
  • 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

avatar for Bjorn Gruning

Bjorn Gruning

University of Freiburg
avatar for Martin Čech

Martin Čech

Dev and Trainer, free element
Galaxy Enthusiast

Tuesday June 26, 2018 9:00am - 11:30am PDT
PAB 320 Performing Arts Building, Reed Campus