galaxyproject / training-material

A collection of Galaxy-related training material

Galaxy Training Material

This repository collects tutorials, slides, and exercises developed and maintained by the Galaxy community.

Usage

The content of the material is developed in Markdown and a templating system (Jekyll) is used to format the tutorials and generate a website (http://training.galaxyproject.org).

Do you want to help with this project? Have a question? Please have a look at our tutorials dedicating to training material development and our FAQ.

If you want to build the website locally, please have a look at the tutorial.

License

The content of the tutorials and website are licensed under the Creative Commons Attribution 4.0 International License.

The code behind the infrastructure is licensed under the MIT License

Acknowledgment and Funding

We would like to thank all contributors, especially those mentioned in the Contributors list, the Galaxy community for their constant support, and our funding partners listed in the GTN

training-material's Issues

Fill the hands-on tutorial and the slides for "Getting to know workflows" and add a Galaxy tour

Hi,

The tutorial on "Getting to know workflows" and the associated slides need to be filled with content and hand-on.

We can take inspiration from "Galaxy 101-2: Getting to know workflows".

We also need to add a Galaxy tour for this tutorial.

Thanks,

Bérénice

Add Bioschemas to all training material to be queried by TeSS

http://bioschemas.org/

Fill the introduction slide deck on Galaxy Introduction

Hi,

The introduction slide deck of Galaxy needs to be filled.
I think it could be nice to use ideas from this slide deck

Thanks

Bérénice

Fill the hands-on tutorial and the slides on "Moving from MySQL to PostgreSQL"

Hi,

For "Moving from MySQL to PostgreSQL", the tutorial and the associated slides need to be filled with content and hand-on.

It can be nice to take inspiration from:

• "Moving from MySQL to PostgreSQL"
• "Moving from MySQL to PostgreSQL"

Thanks,

Bérénice

(Native) English proofreading of CONTRIBUTING

☝ Newcomers Only

This issue is reserved for people who never contributed to Open Source before.
We know that the process of creating a Pull Request is the biggest barrier for new contributors.

❓ The Motivation

As most of our contributors are non-native English speakers/writers, we are looking for people willing to proofread the training material.

🎯 The goal

The CONTRIBUTING.md needs to check to find spelling or syntax errors.

📋 Step by Step

1. Claim this issue by commenting below
2. Edit the CONTRIBUTING.md with your changes after clicking on small ✏️ in the top right)
3. Propose file change with the message Fix spelling/syntax errors in CONTRIBUTING
4. Ask in comments for a review :)
5. 🏁 Done

If you are familiar with the terminal or would like to learn it, you can follow the GitHub flow for 2 and 3:

• Create a fork of this repository on GitHub
• Clone your fork of this repository to create a local copy on your computer
• Create a new branch in your local copy for each significant change
• Commit the changes in that branch
• Push that branch to your fork on GitHub
• Submit a pull request from that branch to the master repository
• If you receive feedback, make changes in your local clone and push to your branch on GitHub: the pull request will update automatically

🤔❓ Questions

Ping us on the Gitter chat

add example about history sharing to the database schema training material

we need a small example explaining what happened when you share a history, and later try to delete datasets from this history

I will take care about this...eventually in time for GCC2017

Add a Galaxy tour

Integrate a template system

We would like to integrate a small template system into our training material. It should be possible to easily compile a training-course PDF with individual logos or funding agencies.
We could also think about changing reference-genomes and the links to training material via templates.

Where to store images?

In a ~/shared/images folder or next to the training material in a ./images folder?

Fill the hands-on tutorial and the slides for Ref based RNA Seq tutorial and add a Galaxy tour

Hi,

The tutorial and the associated slides on Ref based RNA-seq needs to be filled.

I thought to combine the two previous tutorials:

• The one used in Freiburg WS
• Reference-based one

For the slide deck, we can take inspiration from slides used in Freiburg WS and also from the first part of Reference-based tutorial

We also need to add a Galaxy tour

Thanks,

Bérénice

RNASeq: de novo transcriptome assembly with Trinity

For the #58 hackathon, I propose to work on some training material for de novo transcriptome assembly with Trinity.
The Trinity wrappers are up to date in IUC, and I have a (not yet public) workflow using them to do assembly+abundance estimation+differential expression.
Any help is welcome of course!

Base the training material on official flavours.

Thinking about our Docker Images, it would probably make sense to base the training image on some official flavors?

https://github.com/bgruening/docker-recipes/tree/master/galaxy-exom-seq

Disadvantage is that in the resulting training container could contain more tools than needed. How bad is this?

ping @bebatut

Fill the hands-on tutorial and the slides on "Tool development and integration into Galaxy"

Hi,

For "Tool development and integration into Galaxy", the tutorial and the associated slides need to be filled with content and hand-on.

As said in #50, it can be nice to take inspiration from:

• Gildas' slides
• Some slides I made for a workshop
• Planemo's tutorial

We can also split the tutorial in two parts like Planeno's one.

@lecorguille You said you plan to work on this during the contribution fest. Do not you?

Bérénice

GUIDELINES.md

We created a few issues over the last days, getting a sense of how we would like to structure the repo and what is recommended and not.
We need to collect this in a GUIDELINES.md file. Any help welcome.

Add training instances and training partners to a map

We need to guide users to our training, the closest one if possible to save the environment.

We already had some attempts to collect this information but no one ever succeed as far as I remember. What do you think about the following idea and make it github based?

https://github.com/bgruening/galaxy-maps

@bebatut @nekrut @hrhotz

Galaxy training contribution fest - 6-7th October

Dear training enthusiast,

The Galaxy Training Network (GTN) is planning a contribution fest to consolidate our training material and improve the overall training experience in Galaxy on the 6.-7th October 2016!

More information about this project can be found here:
https://gist.github.com/bgruening/a54a8600c5cddca82424ad13569708c3

and a small presentation is here:
http://bgruening.github.io/training-material/shared/slides/project_presentation#/

This will be an online contribution fest and the fun to contribute should be priority one! There is enough to work on in all areas, from programming to fix spelling mistakes. So everyone is welcome to improve the Galaxy training material.

Organisation

We will coordinate ourselves over Gitter: https://gitter.im/Galaxy-Training-Network/Lobby
In addition we will be available at this hangout https://hangouts.google.com/call/bapluwa3s5deveo5flrcwqzqpme
A list of this that can be worked on during the contribution fest can be found here: https://github.com/bgruening/training-material/issues

How to start contributing?

A small checklist to help you with this contribution fest

• Create a GitHub account
• Check the CONTRIBUTING.md
• Become familiar with this repository structure
• Connect to the Gitter chat with your GitHub account and say hello :)
• Check out the issues and PR
• Add you on the CONTRIBUTORS.md
• Add you on the Galaxy map
• Register for the hacktoberfest
• (If you like) Assign yourself as a maintainer of a topic and take over responsibilities
• Assign yourself to an issue or a PR when you find one (or create one) and tell it on Gitter
• Ask if you have any question

Ciao,
Bérénice and Bjoern

Fill the hands-on tutorial and the slides for "Dive into quality control" and add a Galaxy tour

Hi,

I started to fill the tutorial and the associated slides on Quality control, with template and idea.

We now need to fill it with a real dataset and hands-on. We can use the one from Chip-Seq or any other.

We also need to add a Galaxy tour

Thanks,

Bérénice

Move the content of [Docker slides](http://galaxy.slides.com/bgruening/the-galaxy-docker-project#/) to `slides/galaxy_docker.html`

Fill the hands-on tutorial and the slides for "Docker for Galaxy"

Hi,

The tutorial on "Docker for Galaxy" and the associated slides need to be filled with content and hand-on.

We can take inspiration from Bjoern's slides

Thanks,

Bérénice

Outline of the training material restructering

As discussed in the GTN BOF at GCC I will start restructuring our training material and define a common scaffold. This will happen in this repository as a playground.

In the readme file I added a few icons and a small description:

https://github.com/bgruening/training-material/blob/master/README.md

This should serve as fast indicator what a user can expect from our training material.

Ideal case: Hands-on training material, with Docker image and Galaxy tours.

I'm in contact with Frederik Coppens (@frederikcoppens) and we should be able to coordinate this with ELIXIR and get some help in restructuring and collection other materials.

As soon as (let's say) the RNA-Seq tutorial has at least a Docker container and we are happy with the structure I will move this repository over to the galaxyproject organization.

Further steps will be the integration of a template system (bgruening#5) and getting tours better integrated.

Fill the hands-on tutorial and the slides on "Visualizations in Galaxy"

Hi,

For "Visualizations in Galaxy", the tutorial and the associated slides need to be filled with content and hand-on.

Documentation about Galaxy visualizations can be used as base:

• https://wiki.galaxyproject.org/VisualizationsRegistry
• https://wiki.galaxyproject.org/VisualizationsRegistry/Cookbook
• https://wiki.galaxyproject.org/VisualizationsRegistry/Code
• https://wiki.galaxyproject.org/DataProviders
• https://wiki.galaxyproject.org/DataProviders/Cookbook
• https://wiki.galaxyproject.org/Develop/Visualizations

Thanks,

Bérénice

Galaxy Dev-Corner - Tool integration

So far, here is what we have in France about Tool integration.
https://www.dropbox.com/s/afoftkt2k103tdx/galaxy4bioinformatics-integration-partI-1.13.pdf?dl=0

We already gave this course during 3 sessions.

I aware that it's not up-to-date about Conda and that I was at that moment a little scare to base all the training on Planemo because it couldn't handle dependencies properly, was a little buggy (or it's was us?) and because we were not so many to correctly use it among the trainers, ...
And I guess it's not either complete about dataset collection.
And ...

I know that there are some on Planemo readthedocs But, is there other materials somewhere?

Format the hands-on tutorial and fill the slides on "Galaxy database schema to the template"

Hi,

The tutorial on Galaxy database schema needs to be formatted to fit the tutorial template recommendations and the associated slides to be filled

Thanks,

Bérénice

Images are not available

No images are loaded in training-material/Genome-Annotation/general-introduction/README.md

Fill the hands-on tutorial and the slides for "Setting up a Galaxy instance"

Hi,

The tutorial for setting up a Galaxy instance and the associated slides need to be filled with content and hand-on.
It can be nice to use the content of 10rules_for_GaaS

Thanks,

Bérénice

create awesome landing page with github pages

Thanks to a pointer from @bebatut to https://github.com/blog/2228-simpler-github-pages-publishing?

We now serve this site http://bgruening.github.io/training-material/ from the master branch.

• setup basic Jekyll page
• figure out how we can update the page content automatically, so that all slides etc are displayed on this side

Slides format?

In which format should we host Slides?
Please vote with thumbs-up or comment with a new format, but offer an explanation.
It should be a source file format, PDF will be auto-generated from that source.

Galaxy Docker flavours for every training

The idea is to offer training Docker Instances for course. We could have a Docker subdir in each training course and build images automatically.

@dyusuf @nekrut what do you think.
We already started with a RNA-workbench and have one for ChIP-seq (mainly the deeptools Image).

Fill the hands-on tutorial and the slides for "Processing many samples at once" and add a Galaxy tour

Hi,

The tutorial on "Processing many samples at once" and the associated slides need to be filled with content and hand-on.

We can take inspiration from "Processing many samples at once".

We also need to add a Galaxy tour for this tutorial.

Thanks,

Bérénice

Fill the introduction slide deck about RNA-seq

Hi,

The introduction slide deck on RNA-Seq needs to be filled.

We can take inspiration from:

• Previous slide deck

Thanks

Bérénice

Build the Docker image for dev-corner

Hi,

The Docker image for Dev-corner need to be build to be available.

Thanks

Bérénice

Fill the introduction slide deck about Development in Galaxy

Hi,

The introduction slide decks Development in Galaxy needs to be filled.
I think it could be nice to give an introduction about Galaxy and what is inside Galaxy. I started by adding a big picture of "Galaxy universe".

Thanks

Bérénice

Fill the introduction slide deck about ChIP-seq

Hi,

The introduction slide deck on ChIP-Seq needs to be filled.

We can take inspiration from:

• https://drive.google.com/file/d/0B9urRnOAUUI8UmwzbTVpdmZucWM/view

Thanks

Bérénice

Fill the hands-on tutorial and the slides for main ChIP-seq tutorial and add a Galaxy tour

Hi,

I started to fill the tutorial and the associated slides for ChIP-seq with previous tutorial content.

We need to end to fill it with previous tutorial content by formatting the content to new templates.
We can also take inspiration from:

• https://drive.google.com/file/d/0B9urRnOAUUI8UmwzbTVpdmZucWM/view
• https://drive.google.com/file/d/0B9urRnOAUUI8cHpzYVBscjNKWEE/view

We also need to add a Galaxy tour

Thanks,

Bérénice

Fill slides on "From MySQL to PostgreSQL"

Hi,

It could be nice to add the content of :

• "Moving from MySQL to PostgreSQL"

• "Moving from MySQL to PostgreSQL"

  to Admin-Corner/slides/mysql_to_postgresql.html.

Bérénice

Into the workbench

let's get the rna-seq page dynamically loaded into the docker build for galaxy-rna-workbench

Fill slides on "Setting up a Galaxy instance"

add admin training material

@hrhotz I will add this issue to you :)

Fill the hands-on tutorial and the slides for "Dive into mapping" and add a Galaxy tour

Hi,

The tutorial and the associated slides on Mapping needs to be filled.

We can use beginning of ChIP seq training as example.
We also need to add a Galaxy tour

Thanks,

Bérénice

Fill the hands-on tutorial and the slides for "Galaxy introduction" and add a Galaxy tour

Hi,

The tutorial on "Galaxy Introduction" and the associated slides need to be filled with content and hand-on.

I thought to combine in this tutorial:

• Previous course "From Peaks to Genes"
• Galaxy 101-1: The first thing you should try

We also need to add a Galaxy tour for this tutorial.

Thanks,

Bérénice

Fill the hands-on tutorial and the slides for "IGV introduction"

Hi,

The tutorial on "Using the Integrative Genomics Viewer" and the associated slides need to be filled with content and hand-on.

We can take inspiration from "Using the Integrative Genomics Viewer".
Thanks,

Bérénice

Need maintainers for each topic

Hi,

We need one or two maintainers for each topic.

A maintainer acts as editors. She is responsible for making sure issues and change requests are looked at. She has the final say over what is included in the training material related to the topic. But, she is not responsible for writing training material content or deciding what lessons ought to exist, both coming from the community.

Are you interested? Do not be shy, everyone can do that :)
Please, answer this issue with your name, your email and the topic(s) you want to maintain

I will keep a track of all propositions (even if there is more than 2 persons for a topic):

• Admin-corner
  • Hans-Rudolf: [email protected], [email protected]
• NGS-QC
  • Markus Wolfien: [email protected]
• NGS-mapping
• ChIP-Seq
  • Friederike Dündar: [email protected]
• Dev-Corner
  • Gildas Le Corguillé
• Exome-Seq
• Genome-Annotation
• Galaxy Introduction
• MethylC-Seq
• RNA-Seq
  • Friederike Dündar: [email protected]

Thanks a lot,

Bérénice

References

I would also move the references to (a separate file) in each folder in stead of in the general readme. I saw for some material there is already a list of references.

Splitting the markdown files will aid the maintainability IMO but will require merging them to generate the pdf.

README.md link broken

Link to Galaxy_Introduction under README.md is broken:
https://github.com/bgruening/training-material/blob/master/Galaxy_Introduction/Galaxy_Introduction.md

Galaxy visualizations

@carlfeberhard was so kind and contributed a list of visualization resources from the Galaxy wiki which are now stored here:

https://github.com/bgruening/training-material/tree/master/Dev-Corner/visualisations

• It would be nice to create a step-by-step tutorial, something like the planemo docs for visualisations here in this repo.
• We should write something about the BioJS cooperation and how we can include BioJS components into Galaxy

Fill the introduction slide deck about NGS-QC

Hi,

I started to fill the introduction slide deck about NGS-QC. The first part still needs to be filled.

Thanks

Bérénice

Build the Docker image for Admin-corner

Hi,

The Docker image for Admin-corner need to be build to be available.

Bérénice

Fill the introduction slide deck about NGS-Mapping

Hi,

The introduction slide deck on NGS-Mapping needs to be filled

Thanks

Bérénice

Fill the introduction slide deck about Administration of Galaxy Servers

Hi,

The introduction slide decks about Administration of Galaxy Servers needs to be filled.

Thanks

Bérénice

Fill the hands-on tutorial and the slides on "Data source integration"

Hi,

For "Data source integration", the tutorial and the associated slides need to be filled with content and hand-on.

Thanks,

Bérénice