docker/README.md

In neuroconductor/ANTsR: ANTs in R: Quantification Tools for Biomedical Images

ANTsR docker

This Dockerfile builds ANTsR using "method1" as described in the main README, with devtools and install_github.

Building and version information

The default is to build the main branch HEAD. You can build a specific version using build args (from ANTsR/docker):

docker build --build-arg antsr_version="v0.5.6.4" -t antsr .

This allows you to control the ANTsR version, but ITKR and ANTsRCore will be built from the latest commit.

From within the container, find the version of all packages and dependencies with

sessioninfo::package_info("ANTsR")

By default, all dependencies are included. To build a minimal set of dependencies, run

docker build --build-arg antsr_dependencies=NA -t antsr .

Running R or Rscript

To run R interactively:

docker run --rm -it antsr

To run Rscript:

docker run --rm antsr Rscript -e 'print("Hello")'

Controlling threads

The default number of threads is 1, override by passing the ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS variable, eg

docker run -e ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=2 ...

neuroconductor/ANTsR documentation built on Oct. 11, 2020, 8:14 a.m.