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Docker.md

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So I am new to docker:

Here's my flow:

  • First I unsuccessfully tried to run the rocker/r-rmd image, but I could not make it work.
  • Next I found this very useful blogpost which pointed to the rocker/verse image and provided a full on tutorial on how to run these things. I browsed through the different images that rocker provides, and I thought rocker/verse is good enough as it contains the whole of tidyverse but also tex tools which I need to run rmarkdown compiling.
  • I pulled this docker image(docker pull rocker/verse), which by default installed the latest available version.
  • Then I run the following command: docker run --rm -p 8787:8787 rocker/verse, and was prompted to enter another command and set a password for my login (!= rstudio), so I used rstudio1. I run the following command to set the password: docker run -e PASSWORD=rstudio1 -p 8787:8787 rocker/rstudio. Then I opened localhost:8787 in my local browser and entered the username rstudio and the password rstudio1. And then BOOM rstudio session opened up in my browser. Super cool!
  • Unfortunately, rocker/verse does not contain rmarkdown, I could install it separately but I would rather use an image straight out of the box and avoid installing any further libraries. So back to rocker/r-rmd!
  • Turns out I am an idiot and something was wrong with the previous rocker/r-rmd installation. I re-installed it, and it works fine:
docker pull rocker/r-rmd
docker run --rm -p 8787:8787 rocker/r-rmd

In this case, this does not actually open anything in localhost:8787, it will just open the docker image and if you have not asked it do anything it would close it straight away. This at first is unsettling.

  • One must always read the documentation of anything. I went to the docker exec documentation and discovered I could run something like: docker run --name rmd --rm -i -t rocker/r-rmd bash and this will open a bash session I can interact with inside my own terminal. Once I am there I can do other things too, I can open an R session, download files from the internet using wget and many other things. At this stage I tested whether rmarkdown and pandoc were available and moved on. Fyi, I can also run something like, docker run --name rmd --rm -i -t rocker/r-rmd R or docker run --name rmd --rm -i -t rocker/r-rmd tex and that will open R or tex directly from the Docker image.
  • At this point I actually wanted to see what the options meant:
  • --name: pretty clear define name of container, otherwise a random one will be generated.
  • --rm: automatically remove the container when it exits
  • -t, --tty: Allocate a pseudo-TTY. No idea what that means. From this site:

What does the tty command do? It prints the name of the terminal you’re using. TTY stands for “teletypewriter.” And more about pseudo-ty in stack-exchange

  • -i, --interactive: Keep STDIN open even if not attached. i.e. allows you to interact with the image, passing input as if it were your terminal.

Now why are all these necessary? I don't know yet

What I've learnt is that if I remove -i I cannot exit the process with Ctrl-D and if I remove -t nothing happens, as no terminal is created I guess.

Most basic use: docker run --name rmd --rm -t -i rocke/r-rmd

  • I can also interact with it from the background, I can append the option -d, --background and then send commands to be executed there:
docker run --name rmd --rm -tid rocker/r-rmd
docker exec rmd echo 'cat' # will print cat to my main terminal