Persistent reproducible reporting by containerization of R Markdown documents.
liftr aims to solve the problem of persistent reproducible reporting. To achieve this goal, it extends the R Markdown metadata format, and uses Docker to containerize and render R Markdown documents.
Install liftr from CRAN:
Or try the development version on GitHub:
|July 27, 2017||BioC 2017 (poster for dockflow.org)||Dana-Farber Cancer Institute, Boston, MA|
|May 20, 2017||The 10th China-R Conference (talk)||Tsinghua University, Beijng, China|
|April 18, 2017||DockerCon 2017 (talk)||Austin Convention Center, Austin, TX|
|December 3, 2015||CRI Bioinformatics Workshop (talk)||The University of Chicago, Chicago, IL|
|July 21, 2015||BioC 2015 (workshop)||Fred Hutchinson Cancer Research Center, Seattle, WA|
To contribute to this project, please take a look at the Contributing Guidelines first. Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.
liftr is free and open source software, licensed under GPL-3.
render_docker()for debugging: when set to
TRUE, it will only return the Docker commands and not actually run them.
render_docker()to automatically clean up dangling containers and images in case the image build or compilation was not successful (#27). We thank Nicolas Roelandt for suggesting this feature (#25).
prune_all_auto()for automatic pruning of dangling containers or images without particular names specified.
install_docker()for guiding the installation of Docker.
check_docker_install()for checking if Docker is properly installed and discoverable.
check_docker_running()for checking if Docker daemon is running.
purge_infowas renamed to
purge_image()are now renamed to
render_docker()to improve rendering speed significantly by caching Docker image layers [#18].
render_docker(). This argument controls whether to output the Docker image and container name into an YAML file for purging purposes later.
purge_image()for cleaning up.
ghpkgfield is now deprecated. The new
remotesfield supports devtools remote package name format. Now packages can be installed from GitHub, Bitbucket, Git/SVN servers, URLs, etc.
includefor including any custom Dockerfile snippets into the final Dockerfile. This also fixes #21.
drender()is now deprecated.
inst/examples/: explore tidyverse and Bioconductor RNA-Seq workflow.
docker runto fix #17.
pandocto control Pandoc installation. Automatically set this to
bioconductor/...images. This solves #12.
drender(). They provide basic support for dockerizing R Markdown documents, with support for running Rabix workflows/tools before rendering R Markdown documents in Docker containers.