Class RExecutor

java.lang.Object
picard.util.RExecutor
public class RExecutor extends Object
Util class for executing R scripts.

  • Field Details

    • GATK_LITE_DOCKER_ENV_VAR

      public static String GATK_LITE_DOCKER_ENV_VAR
      Name for the environment variable / system property that indicates this is running in the GATK-Lite Docker image. This is referenced to determine whether R is available.

  • Constructor Details

    • RExecutor

      public RExecutor()

  • Method Details

    • executeFromClasspath

      public static int executeFromClasspath(String rScriptName, String... arguments)
      Executes the given R script that is stored in a file on the classpath. The script file is read from the classpath and written to a temp file then executed by a call to Rscript. Blocks until the R script is complete.
      Parameters:
      rScriptName - the fully qualified name of the classpath resource of the script
      arguments - any arguments required by the script
      Returns:
      the return code of the R process

    • executeFromFile

      public static int executeFromFile(File scriptFile, String... arguments)
      Executes the given R script that is stored in a file by a call to Rscript. Blocks until the R script is complete.
      Parameters:
      scriptFile - the file object for the script
      arguments - any arguments required by the script
      Returns:
      the return code of the R process

    • runningInGatkLiteDocker

      public static boolean runningInGatkLiteDocker()
      Checks for the environment variable / property that indicates this is running in the GATK-Lite Docker image.
      Returns:
      true if the environment variable or property is set and is true, false otherwise