containers-course

Course on Linux containers for scientific environments.

Editions

• June 13-14, 2019. CRG, Barcelona, Spain. Slides and hands-on repository by Carlos Eduardo Arango Gutierrez
• January 28-29, 2019. CRG, Barcelona, Spain. Slides and Web seminar by Dave Godlove (associated material)
• December 11-12, 2018. CRG, Barcelona, Spain. Slides

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

  • Examples
    • NCBI Blast+
    • Venn Diagram R script
    • Possible exercise: Trimmomatic (http://www.usadellab.org/cms/?page=trimmomatic)
    • Possible exercise: Samtools (http://www.htslib.org/)

• Volumes

  • Using sequences. From http://www.uniprot.org

  • Using Database. Example: Swissprot from NCBI - FASTA files

• 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

  • NCBI Blast+ with PHP script
  • Possible exercise: Repeat the same with Samtools or Trimmomatic
  • Possible exercise: Play with Shiny App examples
    • https://github.com/LJI-Bioinformatics/Shiny-PCA-Maker
    • https://github.com/philippmuench/Donut

• 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