Preperation

Bioinformatics_2020Fall requires for basic commmonds of R and Linux as well as set up of coding environment for the convinience of integrated software packages (e.g. Docker & Singularity), and this chapter summarize

• -

Docker

• Download Docker for corresponding system (Mac/Linux/Win 10 pro)
• Download Docker image
• Install & Container

  docker load -i ~/Desktop/bioinfo_xxxx.tar.gz
  #load image from absolute path
  mkdir ~/Desktop/bioinfo_tsinghua_share  
  #create image path on desktop
  docker run --name=bioinfo_tsinghua -dt  -h bioinfo_docker --restart unless-stopped -v ~/Desktop/bioinfo_tsinghua_share:/home/test/share bioinfo_tsinghua
  #create a container
  

  Shared dir for host and container ~/Desktop/bioinfo_tsinghua_share == /home/test/share

• Run & Exit

  docker exec -it bioinfo_tsinghua bash
  #start the container
  exit
  #quit the container
  

• Maintain

  docker info #check if docker is correctly installed
  docker ps #checking running container
  docker ps -a #check all container
  docker image #check all images
  docker rm -f bioinfo_tsinghua #remove container
  docker rmi bioinfo_tsinghua #remove image
  

Cluster & Singularity

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