Developer documentation

Installation

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

downloading a container

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

docker pull neuroinformatics/boldqc

or you can pull a specific version e.g., 0.1.0 by running

docker pull neuroinformatics/boldqc:0.1.0

building a container

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

docker build -t boldqc:latest - < Dockerfile

Now you can run boldQC.py—which is the default ENTRYPOINT—using docker run

docker run boldqc:latest --help

Note

You can also convert the BOLDQC Docker image into a Singularity image, however to run boldQC.py you’ll need to supply --pwd /sw/apps/boldqc

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

XNAT Installation

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

building the plugin

Clone the xnat-1.8 branch from the github.com/harvard-nrg/boldqc repository

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

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/boldqc-plugin-1.0.0.jar ${XNAT_HOME}/plugins/