ganga-skrt

This package provides scikit-rt components for the Ganga job-management framework.

The main Ganga repository is:

• https://github.com/ganga-devs/ganga.

For general information on using Ganga, see:

• Ganga User Guide.

Installation

The following have been tested using python 3.8.13, pip 22.3.1, conda 22.9.0 and git 2.28.0.

The recommended installation is using git, conda and pip:

• Clone ganga-skrt and scikit-rt repositories:

  git clone https://github.com/kh296/ganga-skrt
  git clone https://github.com/scikit-rt/scikit-rt
  

• Create and activate ganga-skrt environment, then add scikit-rt:

  cd ganga-skrt
  conda env create --file environment.yml
  conda activate ganga-skrt
  pip install -e ../scikit-rt
  

• Create Ganga configuration file (~/.gangarc):

  create_config
  

Running example

• With the ganga-skrt environment activated, navigate to the directory of example applications, and create a runtime setup script (skrt_conda.sh):

  cd examples/application
  create_setup 
  

• Edit simple_application.py so that the function get_data_locations() returns lists of directories and search patterns that allow identification of patient datasets available on the machine(s) where the application will run.

• Start ganga session:

  ganga
  

• From inside ganga session, submit example job:

  ganga simple_application.py