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Disabled ExampleUG Queue Tests, fixed internal extensions dependency. 

EUG tests disabled due to new protected qscript directory path, post GATK artifact splitting.
This commit is contained in:
Khalid Shakir 2014-05-27 16:16:53 -04:00
parent 3696c2d817
commit 6c9e68ef41
1 changed files with 8 additions and 5 deletions
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13
protected/gatk-queue-extensions-distribution/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleUnifiedGenotyperQueueTest.scala
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@ -50,8 +50,11 @@ import org.testng.annotations.{DataProvider, Test}
import org.broadinstitute.gatk.queue.pipeline.{QueueTest, QueueTestSpec} import org.broadinstitute.gatk.queue.pipeline.{QueueTest, QueueTestSpec}
import org.broadinstitute.gatk.utils.BaseTest import org.broadinstitute.gatk.utils.BaseTest
/*
* TODO: Tests are all currently disabled until we fix the paths to use the qscript directory, or as a patch the gatk.basedir as a passed in variable.
*/
class ExampleUnifiedGenotyperQueueTest { class ExampleUnifiedGenotyperQueueTest {
@Test(timeOut=36000000) @Test(timeOut=36000000, enabled=false)
def testUnifiedGenotyper() { def testUnifiedGenotyper() {
val spec = new QueueTestSpec val spec = new QueueTestSpec
spec.name = "unifiedgenotyper" spec.name = "unifiedgenotyper"
@ -73,7 +76,7 @@ class ExampleUnifiedGenotyperQueueTest {
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", timeOut=36000000) @Test(dataProvider = "ugIntervals", timeOut=36000000, enabled=false)
def testUnifiedGenotyperWithIntervals(intervalsName: String, intervalsPath: String) { def testUnifiedGenotyperWithIntervals(intervalsName: String, intervalsPath: String) {
val spec = new QueueTestSpec val spec = new QueueTestSpec
spec.name = "unifiedgenotyper_with_" + intervalsName spec.name = "unifiedgenotyper_with_" + intervalsName
@ -86,7 +89,7 @@ class ExampleUnifiedGenotyperQueueTest {
QueueTest.executeTest(spec) QueueTest.executeTest(spec)
} }
@Test(timeOut=36000000) @Test(timeOut=36000000, enabled=false)
def testUnifiedGenotyperNoGCOpt() { def testUnifiedGenotyperNoGCOpt() {
val spec = new QueueTestSpec val spec = new QueueTestSpec
spec.name = "unifiedgenotyper_no_gc_opt" spec.name = "unifiedgenotyper_no_gc_opt"
@ -102,7 +105,7 @@ class ExampleUnifiedGenotyperQueueTest {
@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", timeOut=36000000) @Test(dataProvider = "resMemReqParams", timeOut=36000000, enabled=false)
def testUnifiedGenotyperResMemReqParam(reqParam: String) { def testUnifiedGenotyperResMemReqParam(reqParam: String) {
val spec = new QueueTestSpec val spec = new QueueTestSpec
spec.name = "unifiedgenotyper_" + reqParam spec.name = "unifiedgenotyper_" + reqParam
@ -115,7 +118,7 @@ class ExampleUnifiedGenotyperQueueTest {
QueueTest.executeTest(spec) QueueTest.executeTest(spec)
} }
@Test(timeOut=36000000) @Test(timeOut=36000000, enabled=false)
def testUnifiedGenotyperLogDirectory() { def testUnifiedGenotyperLogDirectory() {
val spec = new QueueTestSpec val spec = new QueueTestSpec
spec.name = "unifiedgenotyper_with_log_directory" spec.name = "unifiedgenotyper_with_log_directory"