Skip to content

Instantly share code, notes, and snippets.

Last active October 17, 2016 15:34
What would you like to do?
GTN - new shared training material and technologies for training!

Dear training enthusiast,

We have started to work on an unification of the Galaxy training material as discussed during the GCC 2016. As a first example we have chosen our Exome-Seq tutorial and have ported it over to give a real world example of how we imagine the next generation of Galaxy training looks like. Look by yourself:

A few highlights

  • Slides are written in reveal.js

With this we can create slides in Markdown, which is convenient to write and to share/improve with GitHub. PDFs can be automatically generated and we plan to do this automatically via Travis CI. Moreover these slides can be viewed with every Web browser, so you can watch them while you are exploring our training material, without downloading anything. An example can be found here:

A reveal.js template is available ( to get started, with on the first slide the GTN logo and some instructions how to use the presentation.

  • Docker container for the training

We want to make Galaxy training scale. This means every trainer should be able to get a training instance with all tools, reference datasets, example input datasets up and running in minutes. For this, every training will have a versioned Docker container which can be easily deployed on clusters, clouds or laptops. Naturally, these training instances are available for everyone at any time, so they can used by the trained people to redo the workshop and then consolidate the learned techniques.

  • Galaxy tours!

Every training should offer an interactive Galaxy tour. This is especially useful if someone wants to train herself. The interactive Galaxy tour will be in the Docker container. Hence someone using the Docker container can start the interactive tour and follows interactively the instructions.

  • Persistence and citability of the training data

All the training data on which your training is based should be persistent and citable. For this we recommend to upload the datasets on Zenodo (in Galaxy training network community). A DOI associated to these datasets will be generated. The datasets can then be downloaded into the Docker container and reused everywhere.

  • Landing page

An initial landing page is generated automatically from the general README file:

Some broader plans we have and we need your comments and help!

  • We would like (and we started) to migrate the other training material in a similar fashion than the Exom-Seq. To get an idea of the current and needed work, check the open PRs on
  • We are planning a contribution-fest to consolidate our training material and improve the overall training experience in Galaxy on the 6.-7th October 2016! We will send an invitation to GOBELT and see if someone from them are also interested.
  • We would like to have the material for RNA-Seq, ChIP-Seq, MethylC-Seq and Genome Annotation updated by the end of this year.
  • We would like to write about this effort a small manuscript to attract more people and to announce the new capabilities of Galaxy training (tours, self-containing training with Docker …).

We will keep a ToDo and discussion list on GitHub under the following URL:

Please contribute to these discussions and help make Galaxy training outstanding in Bioinformatics!

Please let us know what you think!

Bérénice and Bjoern

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment