How to configure a custom Dockerfile and run it locally?

21

OK, I was able to proceed by executing the command in a terminal inside the docker container, but the permissions still trip me up, because I cannot install anything inside the container. For example I get an error message that the following folder is not writable:

s -al /layers/paketo-buildpacks_conda-env-update/conda-env/lib/R/
total 116
drwxr-xr-x  10 renku_build cnb  4096 Jan  1  1980 .
drwxr-xr-x  32 renku_build cnb 53248 Jan  1  1980 ..
-rw-r--r--   1 renku_build cnb 18011 Jan  1  1980 COPYING
-rw-r--r--   1 renku_build cnb    46 Jan  1  1980 SVN-REVISION
drwxr-xr-x   3 renku_build cnb  4096 Jan  1  1980 bin
drwxr-xr-x   4 renku_build cnb  4096 Jan  1  1980 doc
drwxr-xr-x   2 renku_build cnb  4096 Jan  1  1980 etc
drwxr-xr-x   3 renku_build cnb  4096 Jan  1  1980 include
drwxr-xr-x   2 renku_build cnb  4096 Jan  1  1980 lib
drwxr-xr-x 113 renku_build cnb  4096 Jan  1  1980 library
drwxr-xr-x   2 renku_build cnb  4096 Jan  1  1980 modules
drwxr-xr-x  11 renku_build cnb  4096 Jan  1  1980 share
 workspace ❯ host ❯ notebooks ▶ docker1 ▶ 1✎ ▶ 2⚑ ▶ $ ▶ whoami
renku

So the owner of the files is renku_build, but the user is renku. I tried running the container as user renku_build, but this led to other errors. Do you have an idea how to solve this?

22

Have you tried just running the container locally as the root user rather than renku_build? Then you will have permissions to do anything inside the container. On renku we run with user and group id 1000. You can try that too.

23

Thanks, but passing --user root to docker run prevents jupyter from starting, and --user 1000 still results in the same permissions problem.

24

Hi @schymans - if you need to just install packages once you are in the session, you can use one of the global environments we provide - either the one using renku/renkulab-r image or one of the rocker images. In the upcoming release we will include an option to automatically build images with R and R packages as well (similar to how it is done now with python).

25

Thanks, Rok, but to make sure that my local docker container behaves similarly to the one on renkulab, I think that running the respective docker image, as proposed by you and @tolevski above would be ideal. There must be a way of fixing the permissions inside the session. Any more ideas?