dockerthis

Ship anything, anywhere!

The main goal of dockerthis is to allow command line applications that don't package nativelly on unsupported Operational Systems (OS) or CPU architectures (e.g. Arm64) to run inside a Linux Docker container.

The main function in this package will try to run the required command line tool in a Ubuntu-based Linux using micromamba to install the required packages, but you can also provide additional Docker Images to for commonly available software.

The development team has a special focus on allowing Bioinformatics.

Installation

You can install the development version of dockerthis using:

remotes::install_github("luciorq/dockerthis")

Example

List files inside a Ubuntu 22.04 LTS container

library(dockerthis)

command_result <- docker_run(
  "ls", "-lah", "/",
  container_name = "dockerthis-ubuntu-test",
  image_name = "ubuntu:22.04"
)

docker_list_containers()

docker_remove_container("dockerthis-ubuntu-test")

command_result

Bionformatics example using the Salmon RNA-Seq Aligner pre-built Docker image, available at COMBINE-lab/salmon.

Automatically remove container after execution.

salmon_result <- docker_run(
  "salmon", "quant", "--help-reads",
  container_name = "dockerthis-salmon-test",
  image_name = "combinelab/salmon:latest",
  docker_args = c(
    "--platform=linux/amd64",
    "--user=",
    "--rm"
  ),
  mount_paths = c(
    getwd()
  )
)

salmon_result

Run any command in a conda environment inside a Linux container leveraging condathis integration with dockerthis.

docker_run(
  "micromamba", "create", "-n", "test-env", "-y", "-c", "conda-forge", "-c", "bioconda", "samtools",
  container_name = "condathis-micromamba-samtools",
  image_name = "luciorq/condathis-micromamba:latest",
  docker_args = c(
    "--platform=linux/amd64",
    "--user=dockerthis",
  ),
  mount_paths = c(
    getwd()
  )
)
docker_remove_container("condathis-micromamba-samtools")

Motivation

dockerthis is an R package that promotes reproducibility and portability by running command line tools within isolated Linux containers. By seamlessly integrating R with Docker, it enables users to create, manage, and execute tools in controlled environments, ensuring consistent execution across different systems and facilitating collaboration. With dockerthis, researchers can confidently share and reproduce their workflows, accelerating scientific discoveries in a wide range of domains.

Considerations

dockerthis don't intend to be a comprehensive Docker Client wrapper. Additionally dockerthis is not intended to be a client communicating directly with the Docker Engine API, for that one can look at projects like stevedore.

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