4.Docker

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Objective: Create Docker image, download packages and Rnotebook

Time estimated: 1 h; taken 2 h;

Date started: 2023-1-18 ; completed: 2023-1-20

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Dockerfile

• Task: Create own Docker image

• Download additional libraries

  • Use a txt file, Dockerfile

  Error, can’t open DockerFile
  Solution, DO NOT use other name, just Dockerfile

  FROM risserlin/bcb420-base-image:winter2023
  
  #Install DESeq2
  RUN R -e "BiocManager::install("DESeq2")'
  
  #Install pheatmap
  RUN install2.r \
      -d TRUE \
      -r 'https://cran.rstudio.com' \
      pheatmap

• Create a container with Dockerfile

  cd /Users/wengjiaming/Documents/BCB420
  docker build -t mybcb420 .
  #name the docker mybcb420

• Run the new Docker

  docker run -e PASSWORD=changeit --rm \
    -v "$(pwd)":/home/rstudio/projects -p 8787:8787 \
      mybcb420

basic RNotebook

• See in DockerAssignment.Rmd

💡Conclusion and outlook: Set up Docker image, note that the name of Dockerfile is important, created the RNotebook and push it to git.

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References

1. Docker
2. Steipe B. and Isserlin R. (2023) R - Basics. https://bcb420-2023.github.io/R_basics/index.html