R script in docker

Question

[mrashad]

Hello,

I am new in docker and try to run this tutorial: https://www.r-bloggers.com/2019/02/running-your-r-script-in-docker/ Through this tutorial, I try to run R script insider the container through the visual studio code. In the first part of tutorial when using the docker file that run the R script manually by source the script from inside the container using:

source("02_code/myScript.R")

It opens the R in terminal inside the visual studio code and the R couldn't see the path of the data, so I tried to change the current working directory using setwd(), it gave me an error that the working directory cannot be changed. I tried to see what is my current directory, I found that it is "/" that I don't know if it is the root or anything else.

I went through the next steps in the tutorial and run the whole R script automatically, the same error appears to me and the path of the input data can't be identified.

Please find the attached photos, the code doesn't run except open the R 4.2 terminal

Your help is appreciated.

Regards

Answer 1

[Jean-Karim Heriche]

This isn't a bioinformatics question. To access data that sits outside the container from within the container, you need to make it accessible within the container. See Docker's documentation on bind mounts.

[mrashad]

Thank you for your answer, it helps me to solve this error.