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Course website "Docker and Singularity for reproducible research: getting started with containers"

Home Page: https://sib-swiss.github.io/containers-introduction-training/

License: Creative Commons Attribution 4.0 International

Dockerfile 31.05% Python 3.46% HTML 51.83% Shell 8.92% R 4.74%
containers docker dockerfile singularity teaching training tutorial

containers-introduction-training's Introduction

GitHub Release Date DOI License: CC BY-SA 4.0

Website is hosted at: https://sib-swiss.github.io/containers-introduction-training/

Please refer to issues for improvements/bugs for course material or the website.

Any contribution to this course material is highly appreciated ๐Ÿ‘. Please have a look at the CONTRIBUTING.md file to learn more on how to contribute.

Course website introduction to containers

Authors

How reuse this material

This website is generated with MkDocs, with the theme Material.

To host it locally, install MkDocs:

pip install mkdocs

and Material:

pip install mkdocs-material

Fork this repository and clone it to your local computer. Then, make the repository your current directory and type:

mkdocs serve

To host it locally.

Check it out with your browser at http://localhost:8000/.

For an automatically generated github page, you can run:

mkdocs gh-deploy

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containers-introduction-training's Issues

Add R examples

Many people have R as 'first language' also provide R examples. (e.g. Rstudio server instead of jupyter and R code instead of python code).

Change introduction

Introduction:

  • Vevox questions -> include question about major programming language (R or python .. )
  • Round of introductions (no google docs needed anymore?)

Extend dockerfile part

More exercises on writing dockerfiles, e.g.:

  • COPY
  • ADD
  • ARG
  • ENV
  • WORKDIR
  • ENTRYPOINT
  • USER

M1 chip issues

Users with an m1 chip can not run their built singularity images. Should be fixed with docker build -t [namespace]/ubuntu-figlet:vx --platform linux/amd64 . However, it needs some testing.

Using the docker container for singularity

When participants push their container to docker hub, and pull it with singularity, using it as a standalone execetuble raises errors:

./ubuntu-figlet-df_v2.sif

This should be adjusted in the exercises

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