Insights! - bcb420-2023/Maryam_Hasanzadehkiabi GitHub Wiki

#Insights:

#Objective: things I want to remember

#Estimated time: working on continuously throughout the term

Opening Docker and RStudio in web browser:

  1. open Terminal

  2. open Docker

  3. input the following command in terminal: docker run -e PASSWORD=changeit --rm -v "$(pwd)":/home/rstudio/projects -p 8787:8787 risserlin/bcb420-base-image:winter2023

  4. went to browser searched: localhistory8787 and entered:

username: rstudio

pass: changeit

To compile for assignments:

  1. open terminal

  2. go to work directory that i have saved the rmd notebook in

  3. double check that the current work directory is correct

  4. copy and paste this command in terminal: docker run --rm -it -v "$(pwd)":/home/rstudio/projects --user rstudio risserlin/bcb420-base-image /usr/local/bin/R -e "rmarkdown::render('/home/rstudio/projects/name_of_rmd.Rmd',output_file='/home/rstudio/projects/name_of_html.html')" > processing_output_filename

  5. change the command above and delete > processing output filename

References

Isserlin, R. (2020). BCB420 - Computational System Biology. Github.Io. https://bcb420-2023.github.io/General_course_prep/

Steipe, B. (2022). R Basics. Github.Io. https://bcb420-2023.github.io/R_basics/ This copyrighted material is licensed under a Creative Commons Attribution 4.0 International License.

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