Commit 5c3e9590 authored by bow's avatar bow
Browse files

Merge branch 'feature-fix_logs' into 'develop'

Feature fix logs

Fix for double logs for BiopetQCommandLine

See merge request !42
parents 3daaba4b 8035d76b
package nl.lumc.sasc.biopet.core
import org.broadinstitute.gatk.queue.util.{ Logging => GatkLogging }
import nl.lumc.sasc.biopet.core.workaround.BiopetQCommandLine
trait PipelineCommand extends MainCommand with GatkLogging {
......
......@@ -24,7 +24,7 @@
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package nl.lumc.sasc.biopet.core
package nl.lumc.sasc.biopet.core.workaround
import java.io.File
import org.broadinstitute.gatk.utils.commandline._
......@@ -32,6 +32,7 @@ import org.broadinstitute.gatk.queue.util._
import org.broadinstitute.gatk.queue.QCommandPlugin
import org.broadinstitute.gatk.queue.QScript
import org.broadinstitute.gatk.queue.QScriptManager
import org.broadinstitute.gatk.queue.util.{ Logging => GatkLogging }
import org.broadinstitute.gatk.queue.engine.{ QStatusMessenger, QGraphSettings, QGraph }
import collection.JavaConversions._
import org.broadinstitute.gatk.utils.classloader.PluginManager
......@@ -43,11 +44,12 @@ import java.net.URL
import java.util.{ ResourceBundle, Arrays }
import org.broadinstitute.gatk.utils.text.TextFormattingUtils
import org.apache.commons.io.FilenameUtils
import nl.lumc.sasc.biopet.core.BiopetExecutable
/**
* Entry point of Queue. Compiles and runs QScripts passed in to the command line.
*/
object BiopetQCommandLine extends Logging {
object BiopetQCommandLine extends GatkLogging {
/**
* Main.
* @param argv Arguments.
......
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