datalad-wrappers (also, with EBRAINS support)

Plain Datalad (without EBRAINS)

This repository contains:

• a Dockerfile for building a Ubuntu container with datalad and git-annex
• an Apptainer definition file ubuntu.def for building a similar container with Apptainer
• a bash wrapper script named datalad that can act as the datalad command or the git-annex command through the Apptainer container

Right now, (Feb 2021) the Apptainer container created with the definition file results in a container with datalad 0.11 while the container created with the Dockerfile has datalad 0.12 . I am not sure how to adjust the definition file in order to get 0.12. Suggestions welcome.

Datalad with EBRAINS

The folder 'ebrains' contains basically the same things as the top level directory, but with the necessary code to build a container that also support the special EBRAINS module for datalad. The dockerfile in there use a more recent Linux distribution, AlmaLinux. See the README.md in there for more information.

Building the image with Docker

cd this_repo
docker build .
docker tag dalatad:ubuntu22  # or whatever tag you prefer

The docker image will need to be given a name, which you can do with the 'docker tag' command. See the docker manual for more information.

Building the image with Apptainer

apptainer build datalad.sif ubuntu.def

Building the apptainer image from the Docker image

An alternative way to create the apptainer image directly is to build it from the local docker image created above.

# Given you tagged the Docker build as 'datalad:ubuntu22' as show above...
apptainer build datalad.sif docker-daemon://datalad:ubuntu22

How to use the wrappers

This repo contains a bash script called simply 'datalad'. It is a wrapper that will act as the datalad command provided that the apptainer image datalad.sif (created by one of the two steps above) is installed at an appropriate location. The script will try to find datalad.sif using the environment variable DATALAD_SIF, or failing that under the exact same directory where the script itself is installed. It's up to you to decide which of these two ways you prefer to deploy the command.

The script can be used to invoke ANY command inside the apptainer container, not just datalad. The name of the script itself will be the command that is invoked inside the container. So you can install the script several time with several names in order to access as many commands as you want from the container. An example of that is provided here by having a symbolic link to it created under the name "git-annex", which means we can invoke the git-annex command from the container.