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:
- Submitted issue so I could be added
- Student Wiki Page created, but may need to change format/add more info
- This is the first entry of my course journal on the repo wiki
also added a link to this page from Home page
- Added links to wiki and repo to the main Student Wiki page
- downloaded and installed docker for Mac (v 4.4.2) from https://www.docker.com/products/docker-desktop
- 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.
- may need to explore docker more, maybe finish the tutorial at https://docker-curriculum.com/
- 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
- https://www.docker.com/products/docker-desktop
- https://docker-curriculum.com/
- Isserlin, R. (2021, December 30). BCB420 - Computational Systems Biology - Docker. Toronto; Quercus.