Question

how can I install packages in docker/R/bioconductor so that they persist?

1

Entering edit mode

anton.kratz ▴ 60

@antonkratz-8836

Last seen 8 months ago

Japan, Tokyo, The Systems Biology Insti…

I am using R/bioconductor under docker (mostly because it is much easier for me to install, and I want to enable future reproducibility by others).

I invoke R/bioconductor like this, so that I can access my local files from within it:

docker run -v $(pwd):/home/rstudio/$USER -p 8787:8787 bioconductor/devel_base

This is working great, but now I want to install an additional package (DESeq2). It installs fine, but everytime I restart the docker image, I need to install DESeq2 again! And it takes a long time to download and install.

Can I somehow install DESeq2 into the docker image of bioconductor/devel_base so that it does persist? I.e. I do not want to install it again every time I start the docker image. Or can I somehow save the docker image with the installed DESeq2 in it? Or what is the best approach?

docker • 5.9k views

ADD COMMENT • link 9.1 years ago anton.kratz ▴ 60

score 3 · Answer 1 · 2015-11-19

3

Entering edit mode

Vincent J. Carey, Jr. 6.7k

@vincent-j-carey-jr-4

Last seen 3 months ago

United States

see bioconductor.org/help/docker for

Modifying the images

There are two ways to modify these images:

Making changes in a running container and then committing them using the docker commitcommand.
Using a Dockerfile to declare the changes you want to make.

The second way is the recommended way. Both ways are documented here.

ADD COMMENT • link 9.1 years ago Vincent J. Carey, Jr. 6.7k

0

Entering edit mode

I tried this but I am not quite there yet. First I invoked a container of devel_base:

docker run -ti bioconductor/devel_base R

Now, in the virtual R, I insall DESeq2:

source("https://bioconductor.org/biocLite.R")
biocLite("DESeq2")

I quite the container:

quit()

And now I commit the image:

docker commit -m "Installed DESeq2" -a "Anton Kratz" 5d22a0b73b46 bioconductor/devel_base:v2

This works, I now have an image devel_base:v2 with DESeq2 installed in it, but now how can I invoke a container of devel_base:v2 so that RStudio is running? If I invoke my original command, just changed to use the new image instead:

docker run -v $(pwd):/home/rstudio/$USER -p 8787:8787 bioconductor/devel_base:v2

then in just starts R (command line), immediately exits, and there is no RStudio running at the port I specified (container is still running).

ADD REPLY • link 9.1 years ago anton.kratz ▴ 60