Commit 650352d4 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Adding classpath and memory to beforeGraph

parent a952d8c4
......@@ -31,6 +31,16 @@ trait BiopetJavaCommandLineFunction extends JavaCommandLineFunction with BiopetC
override def javaOpts = super.javaOpts +
optional("-Dscala.concurrent.context.numThreads=", threads, spaceSeparated = false, escape = false)
override def beforeGraph(): Unit = {
if (javaMemoryLimit.isEmpty && memoryLimit.isDefined)
javaMemoryLimit = memoryLimit
if (javaMainClass != null && javaClasspath.isEmpty)
javaClasspath = JavaCommandLineFunction.currentClasspath
threads = getThreads(defaultThreads)
}
/** Creates command to execute extension */
def cmdLine: String = {
preCmdInternal()
......
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