Running scripts

For local/manual installations

• In a terminal, navigate to the directory containing the config file you want to run
• Run the desired script with Rscript: Rscript ~/kboolnet_scripts/VerifyModel.R VerifyModelConfig.R
  • replace ~/kboolnet_scripts/ with the directory where the scripts were installed during setupKboolnet()
  • replace VerifyModel.R with the desired script name
  • replace VerifyModelConfig.R with the name of the config file you are running
• More details about usage are available on each script's wiki page
• Example rxncon models and configuration files for most scripts can be found in examples/ within the script install directory

For Docker installations

• In a terminal, navigate to the directory containing the config file you want to run
• Run the desired script using Docker: docker run -v .:/mnt kboolnet Rscript /root/kboolnet_scripts/VerifyModel.R VerifyModelConfig.R
  • replace VerifyModel.R with the desired script name
  • replace VerifyModelConfig.R with the name of the config file you are running
  • IMPORTANT NOTE: Each Docker container essentially has its own file system. As such, the container can only "see" host files and directories which are explicitly mounted using the -v <host directory>:<container directory> flag. This means that using absolute paths in the config file for a script will not work! Please use relative paths instead.
• More details about usage are available on each script's wiki page
• Example rxncon models and configuration files for most scripts can be found in inst/scripts/examples within the kboolnet repository