Administration Guide

Installation

Recommendation

Unless you have a strong reason to build the container yourself, it is recommended that you download one of the prebuilt containers.

You can install AnatQC either by downloading one of the prebuilt containers, or by building the container manually.

Downloading the container

There are prebuilt versions of AnatQC hosted on GitHub Container Registry. You can pull any specific version of AnatQC by running the following command

docker pull ghcr.io/harvard-nrg/anatqc:0.6.0

If you are using Apptainer/Singularity, use the following command instead

singularity build anatqc.sif docker://ghcr.io/harvard-nrg/anatqc:0.6.0

Building the container

To build AnatQC as a container, grab the latest Dockerfile from the AnatQC Repository and run the following command

docker build -t anatqc:latest - < Dockerfile

After building the container, you should be able to execute AnatQC with docker

docker run anatqc:latest --help

XNAT Integration

The following section will describe how to integrate AnatQC into your XNAT installation by building, installing, and configuring the plugin.

Building the plugin

Clone the xnat-1.8 branch from the AnatQC repository

git clone -b xnat-1.8 --single-branch https://github.com/harvard-nrg/anatqc

XNAT plugins are built using Gradle. Change your working directory into the repository directory, and compile the plugin

cd anatqc
./gradlew jar

Once the plugin has been successfully 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

Important note

Following this documentation section assumes you have successfully downloaded one of the prebuilt container images, or you have built the container image manually, and you have the container image available within a local Docker daemon e.g., unix:///var/run/docker.sock running 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 dialog box where you can configure your command. Paste the contents from command.json

Now, navigate to your Project home page and click on Project Settings in the Actions box. Select Configure Commands and enable the new command for your project

You are now ready to run the AnatQC pipline from the XNAT user interface!