Bioconductor docker images without Rstudio-server?

Question: Bioconductor docker images without Rstudio-server?

3.0 years ago by

USA

Dear BioC team,

I noticed that all of the BioC docker images are based on the rocker/rstudio image, which contains Rstudio-server. I am a big fan of Rstudio's products myself, but Rstudio-server uses the AGPL licsense, which cannot be used within certain commercial organizations.

Given that Rstudio-server is not a prerequisite for using Bioconductor packages, would it be possible to provide docker images based on the rocker/r-base, which does not contain the Rstudio-server product, as well (or even instead)? That way, the docker images would be useful to the largest possible number of users, even within organizations that don't allow the AGPL license.

Many thanks for taking this suggestion under consideration,

Thomas

P.S.: I noticed that the rocker/rstudio Dockerfile also installs some system-wide libraries used by Bioconductor packages, e.g. the libcurl4-openssl-dev libraries are required by RCurl. This instruction would therefore needed to be added to the bioconductor/base Dockerfile(s).

docker

ADD COMMENT • link •

modified 2.5 years ago by Dan Tenenbaum ♦♦ 8.2k • written 3.0 years ago by Thomas Sandmann • 60

2.5 years ago by

Dan Tenenbaum ♦♦ 8.2k

United States

Dan Tenenbaum ♦♦ 8.2k wrote:

The docker containers could be based on r-base, but then people might complain that they don't have RStudio.

So I guess it's a question of what is more valuable to more people, being able to use RStudio out of the box with Biooconductor Docker containers, or not having RStudio in order to comply with licensing requirements.

As it is, your options are to simply not use RStudio, or to make your own images based on our images, in which you remove RStudio.

Also, RStudio has this in a FAQ:

"If it turns out you can’t use AGPL software, we provide a commercial desktop license that comes with support and Pro editions of RStudio Server and Shiny Server that offer additional features around scaling, authentication, and monitoring."

Not sure if that helps you.

ADD COMMENT • link written 2.5 years ago by Dan Tenenbaum ♦♦ 8.2k

Thank you, Dan. I agree that the number of people benefiting from RStudio server is large. I will follow your advice and build my own images.

That said, docker makes it pretty easy to add a layer; removing one isn't as convenient. Starting with r-base, adding Bioconductor and - in a final layer - RStudio would've yielded the same useful product, but would've facilitated making intermediate images (e.g. without RStudio) available.

I am in awe of the automatic build scripts that that you created and it's probably not worth trying to change them at this point. But perhaps that's food for thought for the next docker project. Thanks a lot for investing so much time and thought in making these great tools available!

ADD REPLY • link written 2.5 years ago by sandmann.t • 40

That would be a bit tricky as we are trying to base our images on rocker's, so it seems best (from our point of view) to start by depending on their rstudio images, and not add rstudio ourselves at the end. Otherwise we don't get the benefit of the work they have already done.

Your Dockerfile can be as simple as:

FROM bioconductor/some_image_name

RUN sudo apt-get remove -y rstudio-server # not sure of the exact package name

ADD REPLY • link written 2.5 years ago by Dan Tenenbaum ♦♦ 8.2k

Completely agree, it makes total sense to take advantage of the work rocker has already invested in installing RStudio server.

Thank you for pointing out that I can include the removal step in my Dockerfile. I hadn't even thought that far, yet. apt-get remove didn't work for me, but

dpkg --remove rstudio-server

removed the tool. Now I can fully benefit from your work :-) Thanks again for making the docker images available!

ADD REPLY • link written 2.5 years ago by sandmann.t • 40

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