Developer documentation

Installation

At the moment, the only supported way to install AnatQC is within a container.

downloading a container

There are prebuilt versions of AnatQC on Docker Hub. You can pull the latest version by running

docker pull neuroinformatics/anatqc

or you can pull a specific version e.g., 0.4.0 by running

docker pull neuroinformatics/anatqc:0.4.0

building a container

To build AnatQC as a container, grab the latest Dockerfile from the repository and run

docker build -t anatqc:latest - < Dockerfile

Now you can run anatQC.py using docker run

docker run anatqc:latest --help

XNAT Installation

The following section will describe how to build and configure AnatQC as a XNAT plugin.

building the plugin

Clone the xnat-1.7.6 branch from the github.com/harvard-nrg/anatqc repository

git clone -b xnat-1.7.6 --single-branch https://github.com/harvard-nrg/anatqc

Change into the repository directory and compile the plugin using Gradle

./gradlew jar

Once the plugin has been compiled, move the resulting .jar into your XNAT plugins directory

mv ./build/libs/anatqc-plugin-1.0.0.jar ${XNAT_HOME}/plugins/

setting up the container

Note

This documentation assumes you have successfully built the container and that the container is being served from a local Docker daemon e.g., unix:///var/run/docker.sock on your XNAT server.

To setup the container within XNAT, go to Administer > Plugin Settings > Images & Commands, find the AnatQC container, and click Add New Command

You should see a small dialog box where you can configure your command. Paste the content from command.json.

Navigate to your Project’s home page and click on Project Settings in the Actions box. Select Configure Commands and enable the new command for your project