R and Docker Set up - bcb420-2023/Maryam_Hasanzadehkiabi GitHub Wiki

initial course set - up

R set-up

1 installed R 2 installed RStudio

Docker set-up

1 Installed Docker

2 created a new image and container

3 opened Terminal and inputed: docker run -e PASSWORD=changeit --rm -v "$(pwd)":/home/rstudio/projects -p 8787:8787 risserlin/bcb420-base-image:winter2023

4 went to browser searched: localhistoryl 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

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