Administration Guide

Installation

Recommendation

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

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

Downloading the container

There are prebuilt versions of BOLDQC hosted on GitHub Container Registry. You can pull the latest version by running

docker pull ghcr.io/harvard-nrg/boldqc:0.7.1

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

singularity build boldqc.sif docker://ghcr.io/harvard-nrg/boldqc:0.7.1

Running with Singularity

To run boldQC.py with Singularity, you'll need to supply --pwd /sw/apps/boldqc

singularity run --pwd /sw/apps/boldqc boldqc.sif --help

Building the container

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

docker build -t boldqc:latest - < Dockerfile

After building the container, you should be able to execute boldQC.py with docker

docker run boldqc:latest --help

XNAT Integration

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

Building the plugin

Clone the xnat-1.8 branch from the BOLDQC repository

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

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

cd boldqc
./gradlew jar

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

mv ./build/libs/boldqc-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 from a local Docker daemon service 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 BOLDQC 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 BOLDQC pipeline from the XNAT user interface!