From a779a6515150cfe4960ec9477eafeebdfa4ff710 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 23 Jun 2014 16:45:57 +0200
Subject: [PATCH] memory multiples by the number of threads
---
.../src/main/scala/nl/lumc/sasc/biopet/function/Pbzip2.scala | 4 ++++
1 file changed, 4 insertions(+)
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Pbzip2.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Pbzip2.scala
index 05b4dcae4..026f9ef27 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Pbzip2.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Pbzip2.scala
@@ -21,6 +21,10 @@ class Pbzip2(val root:Configurable) extends BiopetCommandLineFunction {
override val defaultVmem = (memory * 2 / 1000) + "G"
override val defaultThreads = 2
+ override def beforeCmd {
+ memory = memory * threads
+ }
+
def cmdLine = required(executeble) +
conditional(decomrpess, "-d") +
conditional(!decomrpess, "-z") +
--
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