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instruction_local_docker_Rstudio.md

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Instructions for running Rstudio locally

To run the docker image with metagenomics packages pre-installed on your laptop/desktop:

  1. First pull the docker image

docker pull brusconi/rstudio_workshop

  1. Pull down the week 21 data/scripts and unzip them:
wget -v -O week_21.tar.gz -L https://wustl.box.com/shared/static/8g2spm9vn8agzlkp2h8l4we1ssfj381p
tar -xzvf week_21.tar.gz
  1. Mount the path where your data is stored when launching your docker image.
docker run --rm -p 8888:8787 -v /path/to/week_21:/home/rstudio/data -e PASSWORD=password brusconi/rstudio_workshop
  1. Now open a browser like chrome and navigate to the URL http://localhost:8888

This will open the rstudio session and you can then login with

Username: rstudio
Password: password
  1. Use RStudio to open the Rmd files from the scripts subdirectory within your directory (that you mounted at /home/rstudio/data) and step through the details. For each of the 3 scripts, make sure to update the paths in the setup section to point to the appropriate locations within the docker image.