From e0ed3259263c71e3fe1e92b2509a5ea740564471 Mon Sep 17 00:00:00 2001
From: Sander Bollen <a.h.b.bollen@lumc.nl>
Date: Thu, 12 Mar 2015 14:12:56 +0100
Subject: [PATCH] Set default h_vmem to 6GB for bedtools coverage (used ~3.5GB
in test run)
---
.../lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala | 2 ++
1 file changed, 2 insertions(+)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala
index 9a4e43f41..caab2715e 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala
@@ -46,6 +46,8 @@ class BedtoolsCoverage(val root: Configurable) extends Bedtools {
if (input.getName.endsWith(".bam")) inputTag = "-abam"
}
+ override val defaultVmem = "6G"
+
/** Returns command to execute */
def cmdLine = required(executable) + required("coverage") +
required(inputTag, input) +
--
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