1.3. Work with Docker/Containerized AFNI

1.3.1. Install the Docker Engine

Notes on installing the Docker Engine on various OSs/platforms are available here:
https://docs.docker.com/engine/install/
For example, I have followed the installation steps for Ubuntu here:
https://docs.docker.com/engine/install/ubuntu/
... and my computer did not burst into flames (yet!).

1.3.2. Use pre-built dockerfile

The continuous integration set up on AFNI’s Github uses CircleCi and pushes to a Docker Hub account when it succeeds (thanks, Dylan and Jakub!). It is built with the Dockerfile in the base directory of the AFNI codebase and uses the CircleCi yml file here.

Get the image

To get the image from the online repository (here, Docker Hub), run:

docker pull afni/afni_make_build

This should only have to be done once.

Sidenote: the list of AFNI-built containers that are distributed on Docker Hub is here:
https://hub.docker.com/u/afni
Here, we show an example using the afni_make_build container; this is the best starting point at present, while afni_cmake_build could be reasonable (if not essentially the same), as well.

Start the container environment

To use the contents of the container, copy+paste:

docker run --rm -ti  afni/afni_make_build

After that, the docker environment should be up and running in that terminal, and which afni should output a value under /opt/.... The non-GUI programs should work fine.

To do that while also mounting your home directory (to access those files), you can run:

docker run --rm -ti  -v ${HOME}:/opt/home  afni/afni_make_build

... after which everything in your typical home directory would be accessible under /opt/home/.

Finally, to do both of those things and to have the ability to open up the GUIs, you could run:

docker run --rm -ti                  \
    --user=`id -u`                   \
    -v /tmp/.X11-unix:/tmp/.X11-unix \
    -e DISPLAY=${DISPLAY}            \
    -v ${HOME}:/opt/home             \
    afni/afni_make_build

(Thanks, Vinai, for many helpful pointers with this!)

Exit the container

Select the terminal and hit Ctrl+d, or type the command exit.

1.3.3. Neurodocker

Please also check out Neurodocker for examples of commands to build Dockerfiles and Singularity with AFNI (thanks, Jakub!):

https://github.com/ReproNim/neurodocker