docker image with VariantAnnotation package?
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Paul Shannon ▴ 460
@paul-shannon-5944
Last seen 11 days ago
United States

A docker image with VariantAnnotation and its dependencies?

I figured my best bet for figuring this out on my own was to examine

https://github.com/Bioconductor/bioconductor_docker/blob/master/Dockerfile

but I see only linux libraries listed there, no list of bioc packages.

Where do I look, what do I examine, in order to find the best Docker image for my purposes? Will I discover that VariantAnnotation is found in neither docker base nor docker core? But maybe somewhere else?

Thank you.

docker • 192 views
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@martin-morgan-1513
Last seen 16 days ago
United States

Hi Paul -- the approach we've taken is to provide an image with the system dependencies required to install 'all of' Bioconductor, and then to make it relatively easy to persist installations across container invocation. So I did

/tmp$ mkdir mylibs
/tmp$ docker run -it --rm -v /tmp/mylibs:/usr/local/lib/R/host-site-library bioconductor/bioconductor_docker:devel R -e "options(Ncpus = 8); BiocManager::install('VariantAnnotation', ask = FALSE)"

Then a quick trip to the coffee shop and when I came back I could quickly

/tmp$ docker run -it --rm -v /tmp/mylibs:/usr/local/lib/R/host-site-library bioconductor/bioconductor_docker:devel R

and have access to my installed packages (also through RStudio). The basics are at http://bioconductor.org/help/docker/#mounting .

One fun thing to note is that at least some packages are installed as 'binaries' from RStudio, hence quickly; we'd like to extend that to Bioconductor packages.

If you were wanting to make a Docker image with VariantAnnotation installed, e.g., to share with less enabled colleagues, then I'd clone the repository you mention, at https://github.com/Bioconductor/bioconductor_docker, edit the install.R script, build the image and push to dockerhub or similar for sharing. Maybe https://bioconductor.org/help/docker/#modify is a little more formal about this approach.

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Thanks, Martin - solid advice.

You might be surprised, given my skepticism many years back, but I now spend a lot of time building shiny apps, deployed with Shiny Proxy in docker containers. So your second strategy is for me.

My main misconception was my lazy guy hope that I'd find a docker image ready made for my needs. Silly egocentrism bites the dust once again!

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