Build and run the dHCP pipeline in docker

** now part of https://github.com/biomedia/dhcp-structural-pipeline **

This repro builds and runs the dHCP pipeline inside a docker container. See https://github.com/DevelopingHCP/structural-pipeline

Once you have docker installed, you can build and execute the entire thing on any platform with a single command.

Install docker

See https://docs.docker.com/engine/installation/linux/docker-ce/ubuntu/

Use docker-ce. Make sure there's no old docker on your system:

sudo apt-get remove docker docker-engine docker.io

We need apt over https:

sudo apt-get install apt-transport-https ca-certificates \
   curl software-properties-common

Add docker's GPG key:

curl -fsSL https://download.docker.com/linux/ubuntu/gpg | \
   sudo apt-key add -

Add the repository:

sudo add-apt-repository \
   "deb [arch=amd64] https://download.docker.com/linux/ubuntu \
   $(lsb_release -cs) \
   stable"

Install docker-ce:

sudo apt-get update
sudo apt-get install docker-ce

Test:

sudo docker run hello-world

Build the pipeline

Ask to build branch v1.1 of the pipeline:

./build.sh v1.1

Run the pipeline

Run the dhcp-pipeline.sh script:

./docker-dhcp-pipeline.sh v1.1 subject1 session1 44 \
  -T2 subject1-T2.nii.gz -T1 subject1-T1.nii.gz -t 8

How it works

The Dockerfile in container/ sets up a base image called build-structural-pipeline containing the build prerequisites: Ubuntu 16.04 (xenial), FSL, and all the build tools. This image is cached and reused between runs, so you only have to build it once.

build.sh then goes into the version subdirectory and in there, using the container, runs the second build.sh script. This fetches the latest version of the dHCP pipeline, checks out the version branch, and runs the dHCP setup.sh.