Docker container with bioconductor and devtools
1
0
Entering edit mode
raven • 0
@raven-22181
Last seen 3.3 years 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 • 989 views
ADD COMMENT
2
Entering edit mode
shepherl 3.8k
@lshep
Last seen 7 hours 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.

ADD COMMENT

Login before adding your answer.

Traffic: 756 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6