Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

build.xml

@@ -891,7 +891,7 @@
 
 
     <!-- Build a package consisting of all supporting files. Don't call this target directly. Call one of the specific packaging targets below -->
-    <target name="package" depends="dist,stage,require.executable" description="bundle up an executable for distribution">
+    <target name="package" depends="require.clean,dist,stage,require.executable" description="bundle up an executable for distribution">
       <mkdir dir="${package.output.dir}" />
       <xslt destdir="${package.output.dir}" style="${package.xml.dir}/CreatePackager.xsl" useImplicitFileset="false">
           <flattenmapper/>
@@ -1011,6 +1011,24 @@
         <delete dir="${pipelinetest.dir}"/>
     </target>
 
+    <!-- Depend on this target if your target requires a clean working directory but you don't want to depend on clean directly -->
+    <target name="require.clean">
+        <condition property="not.clean">
+            <or>
+                <available file="${build.dir}" />
+                <available file="${lib.dir}" />
+                <available file="${contract.dump.dir}" />
+                <available file="${staging.dir}" />
+                <available file="${dist.dir}" />
+                <available file="${pipelinetest.dir}" />
+                <available file="${javadoc.dir}" />
+                <available file="${scaladoc.dir}" />
+                <available file="${gatkdocs.dir}" />
+            </or>
+        </condition>
+        <fail message="Selected build target requires a clean working directory. Run ant clean and then try again." if="not.clean" />
+    </target>
+
 
     <!-- ******************************************************************************** -->
     <!-- gsalib                                                                           -->

public/scala/test/org/broadinstitute/sting/queue/pipeline/DataProcessingPipelineTest.scala

@@ -28,7 +28,7 @@ import org.testng.annotations.Test
 import org.broadinstitute.sting.BaseTest
 
 class DataProcessingPipelineTest {
-  @Test
+  @Test(timeOut=36000000)
   def testSimpleBAM {
     val projectName = "test1"
     val testOut = projectName + ".exampleBAM.bam.clean.dedup.recal.bam"
@@ -45,7 +45,7 @@ class DataProcessingPipelineTest {
     PipelineTest.executeTest(spec)
   }
 
-  @Test
+  @Test(timeOut=36000000)
   def testBWAPEBAM {
     val projectName = "test2"
     val testOut = projectName + ".exampleBAM.bam.clean.dedup.recal.bam"

public/scala/test/org/broadinstitute/sting/queue/pipeline/PacbioProcessingPipelineTest.scala

@@ -28,7 +28,7 @@ import org.testng.annotations.Test
 import org.broadinstitute.sting.BaseTest
 
 class PacbioProcessingPipelineTest {
-  @Test
+  @Test(timeOut=36000000)
   def testPacbioProcessingPipeline {
     val testOut = "exampleBAM.recal.bam"
     val spec = new PipelineTestSpec

public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/DevNullOutputPipelineTest.scala

@@ -53,7 +53,7 @@ import org.broadinstitute.sting.queue.pipeline.{PipelineTest, PipelineTestSpec}
 import org.broadinstitute.sting.BaseTest
 
 class DevNullOutputPipelineTest {
-  @Test
+  @Test(timeOut=36000000)
   def testDevNullOutput() {
     val spec = new PipelineTestSpec
     spec.name = "devnulloutput"

public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountLociPipelineTest.scala

@@ -29,7 +29,7 @@ import org.broadinstitute.sting.queue.pipeline.{PipelineTest, PipelineTestSpec}
 import org.broadinstitute.sting.BaseTest
 
 class ExampleCountLociPipelineTest {
-  @Test
+  @Test(timeOut=36000000)
   def testCountLoci() {
     val testOut = "count.out"
     val spec = new PipelineTestSpec

public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountReadsPipelineTest.scala

@@ -29,7 +29,7 @@ import org.broadinstitute.sting.queue.pipeline.{PipelineTest, PipelineTestSpec}
 import org.broadinstitute.sting.BaseTest
 
 class ExampleCountReadsPipelineTest {
-  @Test
+  @Test(timeOut=36000000)
   def testCountReads() {
     val spec = new PipelineTestSpec
     spec.name = "countreads"

public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleReadFilterPipelineTest.scala

@@ -77,7 +77,7 @@ import org.broadinstitute.sting.queue.pipeline.{PipelineTest, PipelineTestSpec}
 import org.broadinstitute.sting.BaseTest
 
 class ExampleReadFilterPipelineTest {
-  @Test
+  @Test(timeOut=36000000)
   def testExampleReadFilter() {
     val spec = new PipelineTestSpec
     spec.name = "examplereadfilter"

public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleRetryMemoryLimitPipelineTest.scala

@@ -29,7 +29,7 @@ import org.broadinstitute.sting.queue.pipeline.{PipelineTest, PipelineTestSpec}
 import org.broadinstitute.sting.BaseTest
 
 class ExampleRetryMemoryLimitPipelineTest {
-  @Test
+  @Test(timeOut=36000000)
   def testRetryMemoryLimit() {
     val spec = new PipelineTestSpec
     spec.name = "RetryMemoryLimit"

public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleUnifiedGenotyperPipelineTest.scala

@@ -29,7 +29,7 @@ import org.broadinstitute.sting.queue.pipeline.{PipelineTest, PipelineTestSpec}
 import org.broadinstitute.sting.BaseTest
 
 class ExampleUnifiedGenotyperPipelineTest {
-  @Test
+  @Test(timeOut=36000000)
   def testUnifiedGenotyper() {
     val spec = new PipelineTestSpec
     spec.name = "unifiedgenotyper"
@@ -51,7 +51,7 @@ class ExampleUnifiedGenotyperPipelineTest {
       Array("vcf_intervals", BaseTest.validationDataLocation + "intervalTest.1.vcf")
     ).asInstanceOf[Array[Array[Object]]]
 
-  @Test(dataProvider = "ugIntervals")
+  @Test(dataProvider = "ugIntervals", timeOut=36000000)
   def testUnifiedGenotyperWithIntervals(intervalsName: String, intervalsPath: String) {
     val spec = new PipelineTestSpec
     spec.name = "unifiedgenotyper_with_" + intervalsName
@@ -64,7 +64,7 @@ class ExampleUnifiedGenotyperPipelineTest {
     PipelineTest.executeTest(spec)
   }
 
-  @Test
+  @Test(timeOut=36000000)
   def testUnifiedGenotyperNoGCOpt() {
     val spec = new PipelineTestSpec
     spec.name = "unifiedgenotyper_no_gc_opt"
@@ -80,7 +80,7 @@ class ExampleUnifiedGenotyperPipelineTest {
   @DataProvider(name="resMemReqParams")
   def getResMemReqParam = Array(Array("mem_free"), Array("virtual_free")).asInstanceOf[Array[Array[Object]]]
 
-  @Test(dataProvider = "resMemReqParams")
+  @Test(dataProvider = "resMemReqParams", timeOut=36000000)
   def testUnifiedGenotyperResMemReqParam(reqParam: String) {
     val spec = new PipelineTestSpec
     spec.name = "unifiedgenotyper_" + reqParam

public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/HelloWorldPipelineTest.scala

@@ -28,7 +28,7 @@ import org.testng.annotations.Test
 import org.broadinstitute.sting.queue.pipeline.{PipelineTest, PipelineTestSpec}
 
 class HelloWorldPipelineTest {
-  @Test
+  @Test(timeOut=36000000)
   def testHelloWorld() {
     val spec = new PipelineTestSpec
     spec.name = "HelloWorld"
@@ -37,7 +37,7 @@ class HelloWorldPipelineTest {
     PipelineTest.executeTest(spec)
   }
 
-  @Test
+  @Test(timeOut=36000000)
   def testHelloWorldWithRunName() {
     val spec = new PipelineTestSpec
     spec.name = "HelloWorldWithRunName"
@@ -47,7 +47,7 @@ class HelloWorldPipelineTest {
     PipelineTest.executeTest(spec)
   }
 
-  @Test
+  @Test(timeOut=36000000)
   def testHelloWorldWithMemoryLimit() {
     val spec = new PipelineTestSpec
     spec.name = "HelloWorldMemoryLimit"
@@ -57,7 +57,7 @@ class HelloWorldPipelineTest {
     PipelineTest.executeTest(spec)
   }
 
-  @Test
+  @Test(timeOut=36000000)
   def testHelloWorldWithPriority() {
     val spec = new PipelineTestSpec
     spec.name = "HelloWorldWithPriority"
@@ -67,7 +67,7 @@ class HelloWorldPipelineTest {
     PipelineTest.executeTest(spec)
   }
 
-  @Test
+  @Test(timeOut=36000000)
   def testHelloWorldWithLsfResource() {
     val spec = new PipelineTestSpec
     spec.name = "HelloWorldWithLsfResource"
@@ -77,7 +77,7 @@ class HelloWorldPipelineTest {
     PipelineTest.executeTest(spec)
   }
 
-  @Test
+  @Test(timeOut=36000000)
   def testHelloWorldWithLsfResourceAndMemoryLimit() {
     val spec = new PipelineTestSpec
     spec.name = "HelloWorldWithLsfResourceAndMemoryLimit"
@@ -87,7 +87,7 @@ class HelloWorldPipelineTest {
     PipelineTest.executeTest(spec)
   }
 
-  @Test
+  @Test(timeOut=36000000)
   def testHelloWorldWithLsfEnvironment() {
     val spec = new PipelineTestSpec
     spec.name = "HelloWorldWithLsfEnvironment"
@@ -97,7 +97,7 @@ class HelloWorldPipelineTest {
     PipelineTest.executeTest(spec)
   }
 
-  @Test
+  @Test(timeOut=36000000)
   def testHelloWorldWithGridEngineResource() {
     val spec = new PipelineTestSpec
     spec.name = "HelloWorldWithGridEngineResource"
@@ -107,7 +107,7 @@ class HelloWorldPipelineTest {
     PipelineTest.executeTest(spec)
   }
 
-  @Test
+  @Test(timeOut=36000000)
   def testHelloWorldWithGridEngineResourceAndMemoryLimit() {
     val spec = new PipelineTestSpec
     spec.name = "HelloWorldWithGridEngineResourceAndMemoryLimit"
@@ -117,7 +117,7 @@ class HelloWorldPipelineTest {
     PipelineTest.executeTest(spec)
   }
 
-  @Test
+  @Test(timeOut=36000000)
   def testHelloWorldWithGridEngineEnvironment() {
     val spec = new PipelineTestSpec
     spec.name = "HelloWorldWithGridEngineEnvironment"