

//
// Here is how you compile and build a commandline executable of proinfer...
//


// Compile

scalac.bat ../*.scala ../proteomics/*.scala



// Create JAR file, proinfer.jar

jar -c -f proinfer.jar -e proteomics.proinfer dbmodel/*.class proteomics/*.class



// Running proinfer using scala.bat on the commandline is possible

scala.bat -cp proinfer.jar proteomics.proinfer ARGUMENTS

scala.bat -cp proinfer.jar proteomics.proinfer ARGUMENTS

scala.bat -cp proinfer.jar proteomics.proinfer --help

scala.bat -cp proinfer.jar proteomics.makedecoys --help



// Running proinfer using java on the commandline is possible in theory.
// However, you need to include lots of Scala libraries.

java -cp 'proinfer.jar;SCALA_LIBRARIES' proteomics.proinfer ARGUMENTS





 
