From a34d5672141d3aed35f0f6effb787d6524652a92 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 19 Jun 2014 10:42:05 +0200
Subject: [PATCH] now uses direct class file
---
.../lumc/sasc/biopet/core/BiopetQCommandLine.scala | 14 ++++++++++----
1 file changed, 10 insertions(+), 4 deletions(-)
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQCommandLine.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQCommandLine.scala
index 19d9a39a2..336a547cb 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQCommandLine.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQCommandLine.scala
@@ -38,6 +38,7 @@ import org.broadinstitute.sting.utils.classloader.PluginManager
import org.broadinstitute.sting.utils.exceptions.UserException
import org.broadinstitute.sting.utils.io.IOUtils
import org.broadinstitute.sting.utils.help.ApplicationDetails
+import java.io.FileOutputStream
import java.net.URL
import java.util.{ResourceBundle, Arrays}
import org.broadinstitute.sting.utils.text.TextFormattingUtils
@@ -97,15 +98,20 @@ class BiopetQCommandLine extends CommandLineProgram with Logging {
private var shuttingDown = false
private lazy val qScriptPluginManager = {
- //qScriptClasses = IOUtils.tempDir("Q-Classes-", "", settings.qSettings.tempDirectory)
+ qScriptClasses = IOUtils.tempDir("Q-Classes-", "", settings.qSettings.tempDirectory)
//qScriptManager.loadScripts(scripts, qScriptClasses)
- var temp: Seq[URL] = Seq()
+ //var temp: Seq[URL] = Seq()
for (t <- scripts) {
- temp :+= this.getClass.getResource(t.toString)
+ val is = getClass.getResourceAsStream(t.getAbsolutePath)
+ val os = new FileOutputStream(qScriptClasses.getAbsolutePath + "/" + t.getName)
+ org.apache.commons.io.IOUtils.copy(is, os)
+ os.close()
+ //temp :+= this.getClass.getResource(t.toString)
+ //logger.info(this.getClass.getResource(t.toString))
val s = if (t.getName.endsWith("/")) t.getName.substring(0, t.getName.length - 1) else t.getName
pipelineName = s + "." + System.currentTimeMillis
}
- new PluginManager[QScript](qPluginType, temp)
+ new PluginManager[QScript](qPluginType, List(qScriptClasses.toURI.toURL))
}
private lazy val qCommandPlugin = {
--
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