→ Slides (10.7490/f1000research.1113243.1)
→ Video
Want to know the big picture about what is going on inside Galaxy? This workshop will give participants a practical introduction to the Galaxy code base with a focus on changing those parts of Galaxy most often modified by local deployers and new contributors.
The workshop will include the following specific content:
Prerequisites:
→ Tutorial
→ Video
This workshop would cover standard, advanced, and alternative RNAseq analysis pipelines, all using workflows and highlighting their advanced features. Three general pipelines would be addressed:
A standard RNAseq analysis pipeline using the Tuxedo suite (Tophat → Cuffdiff) for standard transcript quantification with a reference transcriptome.
An advanced analysis pipeline using the Tuxedo suite with StringTie to create de novo transcript structures, merge these with reference transcripts to create a transcripteome database, followed by transcript quantification.
These three pipelines would be used as examples to highlight usage of workflows and their advanced features.
Prerequisites:
A general knowledge of Galaxy (for example, you should be familiar with the material in Galaxy 101 or have attended Introduction to Galaxy).
A developer school is planned in January 2017, in Strasbourg, organized by Elixir (European bioinformatics HUB) and the French Institute of Bioinformatics (the Elixir French national node). This BoF is a discussion in order to fix training modules that will be proposed. The first discussion about this event has been animated around these slides, during the all-hands Elixir meeting in Barcelona, 2016.
And, if you are interested in proposing a BoF, please submit your idea here and we'll add it to the schedule.
→ Tutorial
This workshop is aimed at people with some experience developing tools and will cover more advanced topics in tool development, more complex tools, and recent enhancements to the Galaxy tool development process including:
Prerequisites:
→ Slides, doi: 10.7490/f1000research.1112914.1
In this session you will get in-depth introduction to Interactive Environments (IE). You will learn how to setup and secure IE’s in a production Galaxy instance. Moreover, we will create an IE on-the-fly to get you started in creating your own Interactive Environments.
Prerequisites:
Following the first Galaxy Data Hackathon at GCC2015, we founded this group to represent the scientific community among Galaxy users. To have a structured voice concerning issues, feedback, needs. To work together and improve conducting Galaxy-based research. We would like to revive this group, so, if you liked what we were doing during the Datathon, but also if you have not been there and would like to contribute to the Galaxy scientific community, please join us.
If you are interested in participating in this BoF, create a Sched login (if you don't already have one), and add this BoF to your personal schedule.
And, if you are interested in proposing a BoF, please submit your idea here and we'll add it to the schedule.
We are interested in a general discussion of Genome Annotation problems and solutions.
If you are interested in participating in this BoF, create a Sched login (if you don't already have one), and add this BoF to your personal schedule.
And, if you are interested in proposing a BoF, please submit your idea here and we'll add it to the schedule.
