VIB Bioinformatics Core training material

This repository collects tutorials, slides, and exercises developed and maintained by VIB Bioinformatics Core.

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://material.bits.vib.be).

License

This work is licensed under the Creative Commons Attribution 4.0 International License.

Development

Materials

Ensure you have docker and docker-compose installed. Login to docker hub (using the vibbioinfocore credentials) using docker login. Then, from this directory, run:

docker-compose up

Jekyll build logs will be displayed. Once completed point your browser to localhost:8080. When you make local changes they should update in your browser automatically. When you want to quit, type Ctrl+c.

By default this process will produce a lot of debug log messages. This is to help you in diagnosing any problems in the site. If you want to silence most of these messages then you will need to edit the docker-compose.yml file. Change the line that reads:

image: vibbioinfocore/training-material:devel

Replace "devel" with "clean". Save. Then run docker-compose up as before.

Docker image

There are two images that are built from Dockerfile.devel and Dockerfile.clean. The following commands will build and publish both tags:

docker build -t vibbioinfocore/training-material:clean -f Dockerfile.clean .
docker push vibbioinfocore/training-material:clean

docker build -t vibbioinfocore/training-material:devel -f Dockerfile.devel .
docker push vibbioinfocore/training-material:devel

For reference, see the Docker documentation on publishing images.

Acknowledgment and Funding

We would like to thank all contributors, especially those mentioned in the Contributors list.

Remarks:

If you add a new contributor for any material, please add this person to the CONTRIBUTOR.md file so that the information needed for the Bioschemas creation is correctly parsed.

Within the conda environment environment.yml you can add a new topic and tutorial with

planemo training_init --topic_name "my-topic" --tutorial_name "my-new-tutorial2" --tutorial_title "Title of the tutorial"

Thereafter, remove any placeholder contributor and replace with the real ones in the files topics/<new topic>/tutorials/<new tutorial>/tutorial.md and topics/<new topic>/slides/introduction.html.

Adapt the file topics/<new topic>/metadata.yaml to follow this template, the keywords for category can be software, omics, basics, advanced, programming, statistics, and admin-dev.

The type must be basics to display the link to the slides and the hands-on materials.

Make sure that the folder metadata contains a symbolic link to the new topic.

---
name: QPCR-analysis-using-qbasePLUS
type: basics
category: software
title: 'QPCR analysis using qbasePLUS'
summary: Summary of the topic
requirements:
maintainers:
- chdeb
references:
- authors: authors et al
  title: the title
  link: link
  summary: ''

Image scaling:

The Markdown for the above could be something like:

![Picture of the Beach -fullwidth](beach.jpg)

-20width width: 20%;

-40width width: 40%;

-50width width: 50%;

-60width width: 60%;

-70width width: 70%;

-75width width: 75%;

-80width width: 80%;

-fullwidth width: 100%;

Another way of scaling and centering images is with HTML code:

<center><img src="https://github.com/vibbits/training-material/raw/master/./../images/plotting1.png" /></center>