0 Account Set Up - bcb420-2023/Helena_Jovic GitHub Wiki

0.0 GitHub Repo and Student Wiki

Objective

  • Set up personal repository on GitHub in bcb420-2023 organization
  • Set up Student Wiki, following Tasks 1-3 in the General Course Prep Unit, which includes setting up a personal Wiki page with the necessary components and a following a guide on how to document journal entries properly.

Time Management

Due 1pm on Friday, January 13th, worth 5%.

Date Started: 2022-01-10
Date Completed: 2022-01-13
Estimated Time: 1h
Actual Time: 1h

Procedure

  1. Submit issue in the Student Wiki repo - issues Links to an external site. with your github name
  2. Set up Student Wiki Page in my personal repo.
  3. Start course journal in my repo wiki.
  4. Add links to your wiki and repo to the main Student Wiki pageLinks to an external site.
  5. Add a category tag to my User page for BCB420. All pages with this tag will be accessible via the link in the sidebar.
  6. Add a copyright template to the bottom of my user page by putting a "This work is licensed under a <a rel="license" href="(https://creativecommons.org/licenses/by/4.0/)." tag on its bottom.
  7. Create an “Insights!” page on a subpage to my User Page and add some placeholder text. That will be expanded when I work through the insights! unit.
  8. Document my progress as a new entry in my journal

No reported issues.

Result

  • Set-up a personal Wiki page with a chosen format, including a personal page, created a couple new journal pages (ready to be filled in), a copyright footer, category tag.
  • Estimated the time needed for this task

Conclusion

Maintain habit of continuously updating course journal as I progress through assignments to improve time-management skills. Next, I will work through the R and Bioinformatic basics units in the course material to prepare for the quiz.

Reference

0.1 Docker Installation

Objective

  • Follow Tasks 3 and 4 in the R Basics unit in the course material to install Docker and create my first notebook saved on local machine

Time Management

Date Started: 2022-01-11
Data Completed: 2022-01-13
Estimated Time: 1.5 hours
Actual Time: 1.5 hours

Procedure

  1. Download and install docker desktop.
  2. Open Terminal
  3. Navigate to directory on your system where you plan on keeping all your code. cd Desktop cd bcb420_code
  4. Run docker run -e PASSWORD=changeit --rm \ -v "$(pwd)":/home/rstudio/projects -p 8787:8787 \ risserlin/bcb420-base-image:winter2022 - This step took the longest, about 20 minutes.
  5. Create your first notebook using Docker
  6. Open a web browser to localhost:8787
  7. enter username: rstudio
  8. enter password: changeit
  9. changing the parameter -e PASSWORD=changeit in the above docker command will change the password you need to specify
  10. After logging in, you will see an Rstudio window just like when you install it directly on your computer. This RStudio will be running in your docker container and will be a completely separate instance from the one you have installed on your machine (with a different set of packages and potentially versions installed).
  11. Create your first notebook in your docker Rstudio.
  12. Make sure all files are put in 'projects' directory in RStudio.
  13. Save it.
  14. Find your newly created file on your computer.

Issues and Resolutions

Issue #1 at Step 4. Received error message: "docker: Cannot connect to the Docker daemon at unix:///var/run/docker.sock. Is the docker daemon running?. After opening Docker on Desktop received error message "docker: Error response from daemon: dial unix docker.raw.sock: connect: no such file or directory. See 'docker run --help'." Opened RStudio on Desktop. Issue #1 Resolved.

Resolution #1: Ensure Docker and RStudio are both open on Desktop when running command at Step 4.

Result

  • Use docker image risserlin/bcb420-base-image following set of instructions including operating system, installed programs and packages.
  • Learn definition for container: "A container is a standard unit of software that packages up code and all its dependencies so the application runs quickly and reliably from one computing environment to another. A container is an instance of an image (we have been provided with an image to use for this course). It is the self-contained running system. There can be multiple containers derived from the same image."
  • Learn definition for docker and docker volumes: "a container platform, similar to a virtual machine but better", "a volume is a way to associate data with a container that will persist even after the container. * maps a drive on the host system to a drive on the container".
  • Save docker notebook onto local machine.

Conclusion

"All assignments for this course are expected to compile and run using the bcb420-base-image:winter2022 docker image to run submitted notebooks. If the notebook runs with no errors and renders your html notebook we will recieve full marks for compilation. It is recommended that we do all your work and assignments using this docker image."

Why are containers great for Bioiformatics?

  • allows you to create environments to run bioinformatis pipelines.
  • create a consistent environment to use for your pipelines.
  • test modifications to the pipeline without disrupting your current set up.
  • Coming back to an analysis years later and there is no need to install older versions of packages or programming languages. Simply create a container and re-run.

Reference

0.2 Journal Template

Objective

Time Management

Date Started:
Date Completed:
Estimated Time:
Actual Time:

Workflow

Result

Conclusion

Reference