diff --git a/public/scala/src/org/broadinstitute/sting/queue/function/JavaCommandLineFunction.scala b/public/scala/src/org/broadinstitute/sting/queue/function/JavaCommandLineFunction.scala index 8cbc2c577..5b19cf9b6 100644 --- a/public/scala/src/org/broadinstitute/sting/queue/function/JavaCommandLineFunction.scala +++ b/public/scala/src/org/broadinstitute/sting/queue/function/JavaCommandLineFunction.scala @@ -72,7 +72,7 @@ trait JavaCommandLineFunction extends CommandLineFunction { null } - def javaOpts = required("-Xmx", javaMemoryLimit.map(gb => (gb * 1024).ceil.toInt), "m", spaceSeparated=false) + + def javaOpts = optional("-Xmx", javaMemoryLimit.map(gb => (gb * 1024).ceil.toInt), "m", spaceSeparated=false) + required("-Djava.io.tmpdir=", jobTempDir, spaceSeparated=false) def commandLine = required("java") +