Create a Simple Bioconductor Container

This function is the main working horse the the package. It creates a container directory and populates it with a Dockerfile and optional data and script directories. The container is ready to be build, pushed and shared with collaborators.

Usage

makeSimpleBiocContainer(
  package = NULL,
  container = "mycontainer",
  data = NULL,
  script = NULL
)

Arguments

package

An optional vector of package names. If not provided, the currently attached packages are used. The function will verify that all the attached packages can be installed from CRAN or Bioconductor and fail otherwise.

container

character(1) with the name of the container. This name will be used to create the directory for the Docker file and optional data and script directories.

data

Optional character() with the path to one or multiple data files to be included in the container in /home/rstudio/data/. Missing files will lead to errors.

script

Optional character() with the path to one or multiple scripts to be included in the container in /home/rstudio/script/. Missing files will lead to errors.

Value

The function returns a character(1) with the path to the container directory. It is used for its side effect of creating and populating the directory. See buildPushDocker() to build and push the container.

Author

SimpleBiocContainer authors

Examples

## Run this in a temporary directory
oldwd <- getwd()
setwd(tempdir())
file.create("data.txt")
#> [1] TRUE
makeSimpleBiocContainer(package = "BiocVersion",
                        data = "data.txt")
#> Creating the container directory 🪐.
#> Creating the Dockerfile 🔔.
#> Adding data.txt 📂
#> Done 👍.
#> [1] "/tmp/Rtmp1z6J3x/mycontainer"
setwd(oldwd)