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Course on Linux containers for scientific environments
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README.md

containers-course

Course on Linux containers for scientific environments.

Editions

Sessions guide

Session 1

  • Introduction to containerization

  • Introduction to Docker

  • Docker Hub. Linux and its diversity. Example to different images. Tags

  • Hands-on testing different images

  • Exporting containers into tar files and importing them back

  • Introduction to software installation

  • Creating Dockerfiles

  • Hands-on testing of different installation methods

  • Volumes

  • Hands-on testing of different images and volumes

  • Services

  • Port mapping and examples with services

  • Different approaches to daemons and services

  • Hands-on with services

  • Hands-on, preparing your own example

Session 2

  • Sum-up last session

  • Putting containers to work together

  • Hands-on example

    • NCBI Blast+ with PHP script + MySQL database
    • Repeat the same with Samtools
  • Docker compose

  • Hands-on example

  • Contributing back your own images. Automated images with Github

  • Introduction to singularity. Differences with Docker

  • Different image types. Different ways to generate images

  • Hands-on in getting images

  • Execution approaches in Singularity

  • Hands-on executing images

  • Singularity files. Custom building of Singularity images

  • Hands-on building of Singularity images

  • Using Docker for building Singularity files

  • Volumes in Singularity

  • Services/instances in singularity

  • Hands-on services with Singularity

  • Sum-up course, finish preparing your own example

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