Docker images

Source: vignettes/docker.Rmd

1 Docker Image with RStudio

We have set up a Docker Image linked to RStudio with Giotto pre-installed.

1.1 Instructions

Follow these instructions to create your own Docker container and run Giotto:

  1. docker pull giottopackage/rstudio_suite:latest
  2. docker run --rm -p 8787:8787 -e PASSWORD=mypassword giottopackage/rstudio_suite:latest
    1. You may use any port as long as it is not in use.
    2. You can set the password to whatever you like.
  3. Open the browser of your choice and enter localhost:yourport.
    1. Where yourport is either 8787 or the port you assigned it in step 2.
  4. You will be directed to an RStudio login.
    1. Username: rstudio
    2. Password: mypassword
      • Note: The password you enter will be whatever you declared in step 2.
  5. Run the following in RStudio:
    1. library(Giotto)
  6. Now you can run any analysis with Giotto!

2 Docker Image with bash terminal

If you prefer to run your analysis directly on the terminal, we have set up a Docker Image able to run in a bash environment.

2.1 Instructions

Follow these instructions to create your own Docker container and run Giotto:

  1. docker pull giottopackage/suite:v4.1.4
  2. docker run -ti giottopackage/suite:v4.1.4 /bin/bash
  3. R
  4. Run the following in R:
    1. library(Giotto)
  5. Now you can run any analysis with Giotto!