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/