Commit ca601520 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added some scala docs

parent b04b3390
...@@ -33,7 +33,11 @@ trait RscriptCommandLineFunction extends BiopetCommandLineFunction { ...@@ -33,7 +33,11 @@ trait RscriptCommandLineFunction extends BiopetCommandLineFunction {
checkScript() checkScript()
} }
def checkScript(local: Boolean = false): Unit = { /**
* If script not exist in file system it try to copy it from the jar
* @param local if true it use File.createTempFile instead of ".queue/tmp/"
*/
protected def checkScript(local: Boolean = false): Unit = {
if (script.exists()) { if (script.exists()) {
script = script.getAbsoluteFile script = script.getAbsoluteFile
} else { } else {
...@@ -53,12 +57,24 @@ trait RscriptCommandLineFunction extends BiopetCommandLineFunction { ...@@ -53,12 +57,24 @@ trait RscriptCommandLineFunction extends BiopetCommandLineFunction {
} }
} }
/**
* Execute rscript on local system
* @param logger How to handle stdout and stderr
*/
def runLocal(logger: ProcessLogger): Unit = { def runLocal(logger: ProcessLogger): Unit = {
checkScript(local = true) checkScript(local = true)
Process(cmdLine).run(logger) Process(cmdLine).run(logger)
} }
/**
* Execute rscript on local system
* Stdout and stderr will go to biopet logger
*/
def runLocal(): Unit = {
runLocal(ProcessLogger(logger.info(_)))
}
def cmdLine: String = { def cmdLine: String = {
required(executable) + required(executable) +
required(script) required(script)
......
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