babelwhale: talk to docker and singularity from R

Specify docker or singularity

library(babelwhale)
config <- create_docker_config()
set_default_config(config)

Run a command in a container

run("alpine", "echo", c("hello"))

## $status
## [1] 0
## 
## $stdout
## [1] "hello\n"
## 
## $stderr
## [1] ""
## 
## $timeout
## [1] FALSE

Get a file from a container

read_file("alpine", "/etc/alpine-release")

## [1] "3.14.0"

Latest changes

Check out news(package = "dynutils") or NEWS.md for a full list of changes.

Recent changes in babelwhale 1.0.3

• BUG FIX detect_backend(): Print helpful message when neither docker or singularity are installed (Thanks @KforKuma).

Recent changes in babelwhale 1.0.2

• BUG FIX test_docker_installation(): Use docker info to check whether docker is available.

• BUG FIX: Redirect stdout and stderr to files to avoid processx hangs (#24, thanks @joelnitta!).

• MINOR CHANGE: Change maintainer from Wouter to Robrecht.

• MINOR CHANGE: Added an environment_variables to the singularity and docker config.