From 1ba03a5e7234f6e5a656801aaf31b7a2fa931500 Mon Sep 17 00:00:00 2001 From: David Roazen Date: Mon, 5 Dec 2011 14:06:00 -0500 Subject: [PATCH] Use optional() instead of required() to construct javaMemoryLimit argument in JavaCommandLineFunction --- .../sting/queue/function/JavaCommandLineFunction.scala | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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") +