Question: Docker container with bioconductor and devtools
0
gravatar for raven
29 days ago by
raven0
raven0 wrote:

Hello,

I am using docker for continuous integration and I need devtools for package building and testing. Is there a docker container available on dockerhub that has both bioconductor configured and devtools installed? This would increase the speed for my building and testing jobs.

Thank you very much.

docker • 55 views
ADD COMMENTlink modified 29 days ago by shepherl ♦♦ 1.7k • written 29 days ago by raven0
Answer: Docker container with bioconductor and devtools
2
gravatar for shepherl
29 days ago by
shepherl ♦♦ 1.7k
United States
shepherl ♦♦ 1.7k wrote:

Not directly as devtools isn't a Bioconductor package and isn't a requirement for Bioconductor packages. However we encourage you to look at the bioconductor_full docker available via dockerhub. It is the bioconductor docker image recommended. You could always update the image locally to install devtools. It is also possible to link a docker image with a local repository of installed packages so it is available for use with the docker image.

 docker run                                     \
      -it                                        \
      --user bioc                                \
      -v ~/host-site-library:/usr/local/lib/R/host-site-library \
      bioconductor/bioconductor_full:devel       \
      R

The -v you would update ~/host-site-library to be the path on your local system where packages are installed to mount to your docker image. If you had devtools installed there, it would be available.

ADD COMMENTlink written 29 days ago by shepherl ♦♦ 1.7k
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