From d1f28ea8825e93dace333cf5c51a35b0963398e6 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 18 Nov 2014 13:29:50 +0100
Subject: [PATCH] Alow for multiple configs in BIOPET_CONFIG and
 BIO_CONFIG_SCATTER

---
 .../lumc/sasc/biopet/core/BiopetQScript.scala |  4 ++++
 .../lumc/sasc/biopet/core/config/Config.scala | 19 ++++++++++++++-----
 2 files changed, 18 insertions(+), 5 deletions(-)

diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
index cf4ee286b..47c7279f5 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
@@ -15,6 +15,9 @@ trait BiopetQScript extends Configurable {
   @Argument(doc = "Output directory", fullName = "output_directory", shortName = "outDir", required = true)
   var outputDir: String = _
 
+  @Argument(doc = "Use scatter defaults, env vale BIOPET_CONFIG_SCATTER", shortName = "SC", required = false)
+  var useScatterDefault: Boolean = false
+
   var outputFiles: Map[String, File] = Map()
 
   var qSettings: QSettings
@@ -25,6 +28,7 @@ trait BiopetQScript extends Configurable {
   var functions: Seq[QFunction]
 
   final def script() {
+    if (useScatterDefault) Config.global.loadDefaultScatterConfig
     if (!outputDir.endsWith("/")) outputDir += "/"
     init
     biopetScript
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
index f6f8e0cf7..c110ea774 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
@@ -12,15 +12,24 @@ class Config(var map: Map[String, Any]) extends Logging {
     loadDefaultConfig()
   }
 
-  def loadDefaultConfig() {
-    var globalFile: String = System.getenv("BIOPET_CONFIG")
-    if (globalFile != null) {
+  def loadConfigEnv(valueName: String) {
+    var globalFiles = System.getenv(valueName).split(":")
+    for (globalFile <- globalFiles) {
       var file: File = new File(globalFile)
       if (file.exists()) {
         logger.info("Loading config file: " + file)
         loadConfigFile(file)
-      } else logger.warn("BIOPET_CONFIG value found but file does not exist, no global config is loaded")
-    } else logger.info("BIOPET_CONFIG value not found, no global config is loaded")
+      } else logger.warn(valueName + " value found but file does not exist, no global config is loaded")
+    }
+    if (globalFiles.isEmpty) logger.info(valueName + " value not found, no global config is loaded")
+  }
+
+  def loadDefaultConfig() {
+    loadConfigEnv("BIOPET_CONFIG")
+  }
+
+  def loadDefaultScatterConfig() {
+    loadConfigEnv("BIOPET_CONFIG_SCATTER")
   }
 
   def loadConfigFile(configFile: File) {
-- 
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