From 709f5517ccdd69ef7d8e90e8efe282167c298c37 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 9 Jun 2014 09:31:18 +0200
Subject: [PATCH] Switched to InProcessFunction, no cluster job needed for ln
commands
---
.../java/nl/lumc/sasc/biopet/wrappers/Ln.scala | 18 ++++++------------
1 file changed, 6 insertions(+), 12 deletions(-)
diff --git a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Ln.scala b/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Ln.scala
index 2764aebf0..a9371cb61 100644
--- a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Ln.scala
+++ b/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Ln.scala
@@ -1,28 +1,22 @@
package nl.lumc.sasc.biopet.wrappers
import nl.lumc.sasc.biopet.core._
-import org.broadinstitute.sting.queue.function.CommandLineFunction
-//import org.broadinstitute.sting.queue.function.QFunction
+import org.broadinstitute.sting.queue.function.InProcessFunction
import org.broadinstitute.sting.commandline._
import java.io.File
import scala.sys.process._
-class Ln(val globalConfig: Config) extends CommandLineFunction {
+class Ln(val globalConfig: Config) extends InProcessFunction {
def this() = this(new Config(Map()))
this.analysisName = "ln"
val config: Config = Config.mergeConfigs(globalConfig.getAsConfig(analysisName), globalConfig)
- logger.debug("Config for " + this.analysisName + ": " + config)
@Input(doc="Input file") var in: File = _
@Output(doc="Link destination") var out: File = _
- def commandLine = {
- "ln -sf " + required(in) + required(out)
+ override def run {
+ val cmd = "ln -s " + in + " " + out
+ val exitcode = cmd.!
+ System.out.println("cmd: '" + cmd + "', exitcode: " + exitcode)
}
}
-
-object Ln {
- def addLn(input:File, output:File) : Ln = {
- return new Ln { this.in = input; this.out = output }
- }
-}
\ No newline at end of file
--
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