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Allow each pipeline test the max of 10 hours to run 

The runtime of these tests is extremely variable -- sometimes they will complete almost instantly,
other times they will wait in an LSF queue for 5-10+ hours. Minimize timeout errors by setting the
timeout for these tests to the maximum of 10 hours.
This commit is contained in:
David Roazen 2012-11-02 12:02:59 -04:00
parent f8a0a947e3
commit 73157ae3d3
9 changed files with 22 additions and 22 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
public/scala/test/org/broadinstitute/sting/queue/pipeline/DataProcessingPipelineTest.scala
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@ -28,7 +28,7 @@ import org.testng.annotations.Test
import org.broadinstitute.sting.BaseTest import org.broadinstitute.sting.BaseTest
class DataProcessingPipelineTest { class DataProcessingPipelineTest {
@Test @Test(timeOut=36000000)
def testSimpleBAM { def testSimpleBAM {
val projectName = "test1" val projectName = "test1"
val testOut = projectName + ".exampleBAM.bam.clean.dedup.recal.bam" val testOut = projectName + ".exampleBAM.bam.clean.dedup.recal.bam"
@ -45,7 +45,7 @@ class DataProcessingPipelineTest {
PipelineTest.executeTest(spec) PipelineTest.executeTest(spec)
} }
@Test @Test(timeOut=36000000)
def testBWAPEBAM { def testBWAPEBAM {
val projectName = "test2" val projectName = "test2"
val testOut = projectName + ".exampleBAM.bam.clean.dedup.recal.bam" val testOut = projectName + ".exampleBAM.bam.clean.dedup.recal.bam"

2
public/scala/test/org/broadinstitute/sting/queue/pipeline/PacbioProcessingPipelineTest.scala
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@ -28,7 +28,7 @@ import org.testng.annotations.Test
import org.broadinstitute.sting.BaseTest import org.broadinstitute.sting.BaseTest
class PacbioProcessingPipelineTest { class PacbioProcessingPipelineTest {
@Test @Test(timeOut=36000000)
def testPacbioProcessingPipeline { def testPacbioProcessingPipeline {
val testOut = "exampleBAM.recal.bam" val testOut = "exampleBAM.recal.bam"
val spec = new PipelineTestSpec val spec = new PipelineTestSpec

2
public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/DevNullOutputPipelineTest.scala
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@ -53,7 +53,7 @@ import org.broadinstitute.sting.queue.pipeline.{PipelineTest, PipelineTestSpec}
import org.broadinstitute.sting.BaseTest import org.broadinstitute.sting.BaseTest
class DevNullOutputPipelineTest { class DevNullOutputPipelineTest {
@Test @Test(timeOut=36000000)
def testDevNullOutput() { def testDevNullOutput() {
val spec = new PipelineTestSpec val spec = new PipelineTestSpec
spec.name = "devnulloutput" spec.name = "devnulloutput"

2
public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountLociPipelineTest.scala
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@ -29,7 +29,7 @@ import org.broadinstitute.sting.queue.pipeline.{PipelineTest, PipelineTestSpec}
import org.broadinstitute.sting.BaseTest import org.broadinstitute.sting.BaseTest
class ExampleCountLociPipelineTest { class ExampleCountLociPipelineTest {
@Test @Test(timeOut=36000000)
def testCountLoci() { def testCountLoci() {
val testOut = "count.out" val testOut = "count.out"
val spec = new PipelineTestSpec val spec = new PipelineTestSpec

2
public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountReadsPipelineTest.scala
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@ -29,7 +29,7 @@ import org.broadinstitute.sting.queue.pipeline.{PipelineTest, PipelineTestSpec}
import org.broadinstitute.sting.BaseTest import org.broadinstitute.sting.BaseTest
class ExampleCountReadsPipelineTest { class ExampleCountReadsPipelineTest {
@Test @Test(timeOut=36000000)
def testCountReads() { def testCountReads() {
val spec = new PipelineTestSpec val spec = new PipelineTestSpec
spec.name = "countreads" spec.name = "countreads"

2
public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleReadFilterPipelineTest.scala
View File

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

2
public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleRetryMemoryLimitPipelineTest.scala
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@ -29,7 +29,7 @@ import org.broadinstitute.sting.queue.pipeline.{PipelineTest, PipelineTestSpec}
import org.broadinstitute.sting.BaseTest import org.broadinstitute.sting.BaseTest
class ExampleRetryMemoryLimitPipelineTest { class ExampleRetryMemoryLimitPipelineTest {
@Test @Test(timeOut=36000000)
def testRetryMemoryLimit() { def testRetryMemoryLimit() {
val spec = new PipelineTestSpec val spec = new PipelineTestSpec
spec.name = "RetryMemoryLimit" spec.name = "RetryMemoryLimit"

8
public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleUnifiedGenotyperPipelineTest.scala
View File

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

20
public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/HelloWorldPipelineTest.scala
View File

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