From 1865f3b0c2defce09768dfd0917c3f3c7ec11c85 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 16 Feb 2015 19:36:04 +0100
Subject: [PATCH] Added default vmem and add log.file as output file
---
.../biopet/extensions/igvtools/IGVToolsCount.scala | 11 +++++++++++
1 file changed, 11 insertions(+)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala
index b62c852f9..4526c2143 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala
@@ -24,6 +24,9 @@ class IGVToolsCount(val root: Configurable) extends IGVTools {
@Output
var wig: Option[File] = None
+ @Output
+ def logFile = new File(jobLocalDir, "igv.log")
+
var maxZoom: Option[Int] = config("maxZoom")
var windowSize: Option[Int] = config("windowSize")
var extFactor: Option[Int] = config("extFactor")
@@ -41,9 +44,17 @@ class IGVToolsCount(val root: Configurable) extends IGVTools {
var pairs: Boolean = config("pairs", default = false)
+ override val defaultVmem = "4G"
+
override def beforeGraph {
super.beforeGraph
+ (tdf, wig) match {
+ case (Some(tdf), _) => jobLocalDir = tdf.getParentFile
+ case (_, Some(wig)) => jobLocalDir = wig.getParentFile
+ case _ => throw new IllegalArgumentException("Must have a wig or tdf file")
+ }
+
wig.foreach(x => if (!x.getAbsolutePath.endsWith(".wig"))
throw new IllegalArgumentException("WIG file should have a .wig file-extension"))
tdf.foreach(x => if (!x.getAbsolutePath.endsWith(".tdf"))
--
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