Docker container with bioconductor and devtools
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raven • 0
@raven-22181
Last seen 8 months ago

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 • 185 views
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shepherl 2.8k
@lshep
Last seen 57 minutes ago
United States

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.

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