Add Github and Bioconductor parameters on create dockerfile function

[brnleehng]

Hi,

Is it possible for us to add github and bioconductor parameters to dockerfile? This would allow us to have a complete Dockerfile.

dockerfile(from = utils::sessionInfo(),
  image = getImageForVersion(getRVersionTag(from)),
  maintainer = Sys.info()[["user"]], save_image = FALSE,
  env = list(generator = paste("containerit",
  utils::packageVersion("containerit"))), soft = FALSE, offline = FALSE,
  copy = NA, container_workdir = "/payload/", cmd = Cmd("R"),
  entrypoint = NULL, add_self = FALSE, vanilla = TRUE, silent = FALSE,
  predetect = TRUE, versioned_libs = FALSE, versioned_packages = FALSE,
  filter_baseimage_pkgs = FALSE,  github_packages = c(), bioconductor_packages = c())

Thanks,
Brian

[brnleehng]

• @nuest

[nuest]

Thanks for pinging, I was on vacation...

In my words, you ask for manually adding packages from github or bioconductor. The thing is, you cannot even do that with CRAN packages currently. So for consistency, a cran_packages = c() parameter would be needed.

Can you elaborate on your use case?

containerit currently focusses on "magically" determining where to install packages from based on what is provided in the from parameter (see code and #101).

[nuest]

Bioconductor is supported in the dev branch: https://github.com/nuest/containerit/blob/dev/vignettes/bioconductor.Rmd