Commit e708d5fa authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Reading of config files now in BiopetExecutable

parent e722a305
package nl.lumc.sasc.biopet.core package nl.lumc.sasc.biopet.core
import java.io.File
import java.util.Properties import java.util.Properties
import nl.lumc.sasc.biopet.core.config.Config
import org.apache.log4j.Logger import org.apache.log4j.Logger
object BiopetExecutable extends Logging { object BiopetExecutable extends Logging {
...@@ -82,6 +84,11 @@ object BiopetExecutable extends Logging { ...@@ -82,6 +84,11 @@ object BiopetExecutable extends Logging {
return command.get return command.get
} }
// Read config files
for (t <- 0 until args.size) {
if (args(t) == "-config" || args(t) == "--config_ile") Config.global.loadConfigFile(new File(args(t + 1)))
}
args match { args match {
case Array("version") => { case Array("version") => {
println("version: " + getVersion) println("version: " + getVersion)
......
...@@ -25,7 +25,6 @@ trait BiopetQScript extends Configurable { ...@@ -25,7 +25,6 @@ trait BiopetQScript extends Configurable {
var functions: Seq[QFunction] var functions: Seq[QFunction]
final def script() { final def script() {
for (file <- configfiles) Config.global.loadConfigFile(file)
if (!outputDir.endsWith("/")) outputDir += "/" if (!outputDir.endsWith("/")) outputDir += "/"
init init
biopetScript biopetScript
......
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