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
* 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: http://bgruening.github.io/training-material
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
Please contribute to these discussions and help make Galaxy training
outstanding in Bioinformatics!
Please let us know what you think!
Bérénice and Bjoern
P.S. If you want to share this news, please take this link: