To use these scripts you need to install either Bioclipse 2.6.2 or Bacting.

After that, you can run the scripts with Groovy. If you are not using Bacting, make sure to remove the following lines at the top of the script:

@Grab(group='io.github.egonw.bacting', module='managers-cdk', version='0.0.33')

workspaceRoot = System.properties['user.dir']
cdk = new net.bioclipse.managers.CDKManager(workspaceRoot);

If you use scripts in this repository, please cite the JOSS article as specified in the CITATION.cff file.