1. Account Set Up - bcb420-2022/RuoXuan_Wang GitHub Wiki

Objective

Set up repository, personal page info, and start journal entries. Install Docker.

Duration

Time estimated: 2 h; taken 4 h;
date started: 2022-01-13; date completed: 2022-01-14

Progress

Tasks:

  1. Submitted issue so I could be added
  2. Student Wiki Page created, but may need to change format/add more info
  3. This is the first entry of my course journal on the repo wiki

also added a link to this page from Home page

  1. Added links to wiki and repo to the main Student Wiki page
  2. downloaded and installed docker for Mac (v 4.4.2) from https://www.docker.com/products/docker-desktop
  3. created a new image and container from the bcb420 Dockerfile
  • navigated to directory for BCB420
  • Using the command docker run -e PASSWORD=changeit -v "$(pwd)":/home/rstudio/projects -p 8787:8787 risserlin/bcb420-base-image:winter2022
  • encountered error: docker: Error response from daemon: error creating temporary lease: write /var/lib/desktop-containerd/daemon/io.containerd.metadata.v1.bolt/meta.db: read-only file system: unknown.
  • worked after checking and clearing space, and restarting docker

Docker:

  • a container platform (similar to virtual machines)
  • creates consistent environment for pipelines/code
  • can test modifications as new environments

Container:

  • an instance of an image
  • so can have multiple from same image
  • image: container blueprint, containing everything the container needs to run
  • VMs need operating system while containers don't
  • VM encapsulates server while Container encapsulates application/service

Docker basics:

  • Dockerfile: remember to add install statements for any additional packages
  • Volumes: stores results - mapping a drive from the host machine to a drive on the container so that files remain
  • Port forwarding: to open communication with host, map a port in the container\
    • To access the container: Open a browser and go to localhost:8787

Conclusion and outlook

  • The required steps were pretty straightforward, but took a long time with the installation and errors encountered during image creation.
  • started going through the 3 sections of preparatory material: General course prep, R Basics, Bioinfo Basics - finish before quiz
    • looks like most may be familiar
    • overlap with BCH441

References