diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
index bf8fe4d041a81d175913eed3fadf2d09b8151c09..f048781a71af2f4ccd3cc78f5202194be2127df0 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
@@ -1,123 +1,15 @@
package nl.lumc.sasc.biopet.core
-import java.io.File
-import org.broadinstitute.sting.queue.QException
-import org.broadinstitute.sting.queue.function.CommandLineFunction
import org.broadinstitute.sting.commandline._
import scala.sys.process._
-import scala.util.matching.Regex
import nl.lumc.sasc.biopet.core.config._
-abstract class BiopetCommandLineFunction extends CommandLineFunction with Configurable {
- analysisName = getClass.getSimpleName
-
- @Input(doc="deps", required=false)
- var deps: List[File] = Nil
-
- @Argument(doc="Threads", required=false)
- var threads = 0
- val defaultThreads = 1
-
- @Argument(doc="Vmem", required=false)
- var vmem: String = _
- val defaultVmem: String = ""
-
- @Argument(doc="Executeble")
- var executeble: String = _
-
- protected def beforeCmd {
- }
-
- protected def afterGraph {
- }
-
- override def freezeFieldValues() {
- checkExecuteble
- afterGraph
- jobOutputFile = new File(firstOutput.getParent + "/." + firstOutput.getName + "." + analysisName + ".out")
-
- super.freezeFieldValues()
- }
-
- protected def checkExecuteble {
- try if (executeble != null) {
- val buffer = new StringBuffer()
- val cmd = Seq("which", executeble)
- val process = Process(cmd).run(ProcessLogger(buffer.append(_)))
- if (process.exitValue == 0) {
- executeble = buffer.toString
- val file = new File(executeble)
- executeble = file.getCanonicalPath
- } else {
- logger.error("executeble: '" + executeble + "' not found, please check config")
- throw new QException("executeble: '" + executeble + "' not found, please check config")
- }
- } catch {
- case ioe: java.io.IOException => logger.warn("Could not use 'which', check on executeble skipped: " + ioe)
- }
- }
-
- final protected def preCmdInternal {
- checkExecuteble
- //for (input <- this.inputs) if (!input.exists) throw new IllegalStateException("Input: " + input + " for " + analysisName + " is missing")
- //logger.debug("Config for " + analysisName + ": " + localConfig)
-
- beforeCmd
-
- addJobReportBinding("version", getVersion)
-
- if (threads == 0) threads = getThreads(defaultThreads)
- if (threads > 1) nCoresRequest = Option(threads)
- addJobReportBinding("cores", if (nCoresRequest.get.toInt > 0) nCoresRequest.get.toInt else 1)
-
- if (vmem == null) {
- if (configContains("vmem")) vmem = config("vmem")
- else if (!defaultVmem.isEmpty) vmem = defaultVmem
- }
- if (vmem != null) jobResourceRequests :+= "h_vmem=" + vmem
- jobName = this.analysisName + ":" + firstOutput.getName
- }
-
+abstract class BiopetCommandLineFunction extends BiopetCommandLineFunctionTrait {
protected def cmdLine: String
final def commandLine: String = {
preCmdInternal
val cmd = cmdLine
addJobReportBinding("command", cmd)
- cmd
- }
-
- protected var versionCommand: String = _
- protected val versionRegex: Regex = null
- def getVersion : String = {
- if (versionCommand == null || versionRegex == null) return "N/A"
- val buffer = new StringBuffer()
- val process = Process(versionCommand).run(ProcessLogger(buffer append _))
- if (process.exitValue != 0) {
- logger.warn("Version command: '" + versionCommand + "' give exit code " + process.exitValue + ", version not found")
- return "N/A"
- }
- val lines = versionCommand lines_! ProcessLogger(buffer append _)
- for (line <- lines) {
- line match {
- case versionRegex(m) => return m
- case _ =>
- }
- }
- logger.warn("Version command: '" + versionCommand + "' give a exit code 0 but no version was found, executeble oke?")
- return "N/A"
- }
-
- def getThreads(default:Int) : Int = {
- val maxThreads: Int = config("maxthreads", 8)
- val threads: Int = config("threads", default)
- if (maxThreads > threads) return threads
- else return maxThreads
- }
-
- def getThreads(default:Int, module:String) : Int = {
- val maxThreads: Int = config("maxthreads", 8, module)
- val threads: Int = config("threads", default, module)
- if (maxThreads > threads) return threads
- else return maxThreads
+ return cmd
}
}
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
new file mode 100644
index 0000000000000000000000000000000000000000..1d6b9091a8209d442b0ed68251cd14b892590f60
--- /dev/null
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
@@ -0,0 +1,115 @@
+package nl.lumc.sasc.biopet.core
+
+import java.io.File
+import nl.lumc.sasc.biopet.core.config._
+import org.broadinstitute.sting.queue.QException
+import org.broadinstitute.sting.queue.function.CommandLineFunction
+import org.broadinstitute.sting.commandline._
+import scala.sys.process._
+import scala.util.matching.Regex
+
+trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurable {
+ analysisName = getClass.getSimpleName
+
+ @Input(doc="deps", required=false)
+ var deps: List[File] = Nil
+
+ @Argument(doc="Threads", required=false)
+ var threads = 0
+ val defaultThreads = 1
+
+ @Argument(doc="Vmem", required=false)
+ var vmem: String = _
+ val defaultVmem: String = ""
+
+ @Argument(doc="Executeble")
+ var executeble: String = _
+
+ protected def beforeCmd {
+ }
+
+ protected def afterGraph {
+ }
+
+ override def freezeFieldValues() {
+ checkExecuteble
+ afterGraph
+ jobOutputFile = new File(firstOutput.getParent + "/." + firstOutput.getName + "." + analysisName + ".out")
+
+ super.freezeFieldValues()
+ }
+
+ protected def checkExecuteble {
+ try if (executeble != null) {
+ val buffer = new StringBuffer()
+ val cmd = Seq("which", executeble)
+ val process = Process(cmd).run(ProcessLogger(buffer.append(_)))
+ if (process.exitValue == 0) {
+ executeble = buffer.toString
+ val file = new File(executeble)
+ executeble = file.getCanonicalPath
+ } else {
+ logger.error("executeble: '" + executeble + "' not found, please check config")
+ throw new QException("executeble: '" + executeble + "' not found, please check config")
+ }
+ } catch {
+ case ioe: java.io.IOException => logger.warn("Could not use 'which', check on executeble skipped: " + ioe)
+ }
+ }
+
+ final protected def preCmdInternal {
+ checkExecuteble
+ //for (input <- this.inputs) if (!input.exists) throw new IllegalStateException("Input: " + input + " for " + analysisName + " is missing")
+ //logger.debug("Config for " + analysisName + ": " + localConfig)
+
+ beforeCmd
+
+ addJobReportBinding("version", getVersion)
+
+ if (threads == 0) threads = getThreads(defaultThreads)
+ if (threads > 1) nCoresRequest = Option(threads)
+ addJobReportBinding("cores", if (nCoresRequest.get.toInt > 0) nCoresRequest.get.toInt else 1)
+
+ if (vmem == null) {
+ if (configContains("vmem")) vmem = config("vmem")
+ else if (!defaultVmem.isEmpty) vmem = defaultVmem
+ }
+ if (vmem != null) jobResourceRequests :+= "h_vmem=" + vmem
+ jobName = this.analysisName + ":" + firstOutput.getName
+ }
+
+ protected var versionCommand: String = _
+ protected val versionRegex: Regex = null
+ def getVersion : String = {
+ if (versionCommand == null || versionRegex == null) return "N/A"
+ val buffer = new StringBuffer()
+ val process = Process(versionCommand).run(ProcessLogger(buffer append _))
+ if (process.exitValue != 0) {
+ logger.warn("Version command: '" + versionCommand + "' give exit code " + process.exitValue + ", version not found")
+ return "N/A"
+ }
+ val lines = versionCommand lines_! ProcessLogger(buffer append _)
+ for (line <- lines) {
+ line match {
+ case versionRegex(m) => return m
+ case _ =>
+ }
+ }
+ logger.warn("Version command: '" + versionCommand + "' give a exit code 0 but no version was found, executeble oke?")
+ return "N/A"
+ }
+
+ def getThreads(default:Int) : Int = {
+ val maxThreads: Int = config("maxthreads", 8)
+ val threads: Int = config("threads", default)
+ if (maxThreads > threads) return threads
+ else return maxThreads
+ }
+
+ def getThreads(default:Int, module:String) : Int = {
+ val maxThreads: Int = config("maxthreads", 8, module)
+ val threads: Int = config("threads", default, module)
+ if (maxThreads > threads) return threads
+ else return maxThreads
+ }
+}
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
new file mode 100644
index 0000000000000000000000000000000000000000..82811a1427d86149260b29bcd8fb12ee73d94f87
--- /dev/null
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
@@ -0,0 +1,15 @@
+package nl.lumc.sasc.biopet.core
+
+import org.broadinstitute.sting.queue.function.JavaCommandLineFunction
+
+abstract class BiopetJavaCommandLineFunction extends JavaCommandLineFunction with BiopetCommandLineFunctionTrait {
+ executeble = "java"
+
+ override def commandLine: String = {
+ preCmdInternal
+ val cmd = super.commandLine
+ val finalCmd = executeble + cmd.substring(cmd.indexOf(" "))
+ addJobReportBinding("command", cmd)
+ return cmd
+ }
+}