From 9644f104c49ed50c8894722ea971d68e274b74ca Mon Sep 17 00:00:00 2001
From: David Roazen <droazen@broadinstitute.org>
Date: Fri, 1 Jul 2011 13:13:24 -0400
Subject: [PATCH] Fixes to the queue pipeline tests to account for the new
 directory structure.

---
 .../pipeline/examples/ExampleCountLociPipelineTest.scala    | 2 +-
 .../queue/pipeline/examples/HelloWorldPipelineTest.scala    | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountLociPipelineTest.scala b/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountLociPipelineTest.scala
index 2b3b51783..09f80f2c3 100644
--- a/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountLociPipelineTest.scala
+++ b/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountLociPipelineTest.scala
@@ -35,7 +35,7 @@ class ExampleCountLociPipelineTest {
     val spec = new PipelineTestSpec
     spec.name = "countloci"
     spec.args = Array(
-      " -S scala/qscript/examples/ExampleCountLoci.scala",
+      " -S public/scala/qscript/examples/ExampleCountLoci.scala",
       " -R " + BaseTest.hg18Reference,
       " -I " + BaseTest.validationDataLocation + "small_bam_for_countloci.bam",
       " -o " + testOut).mkString
diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/HelloWorldPipelineTest.scala b/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/HelloWorldPipelineTest.scala
index 8b8fa86a4..37531e791 100644
--- a/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/HelloWorldPipelineTest.scala
+++ b/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/HelloWorldPipelineTest.scala
@@ -32,7 +32,7 @@ class HelloWorldPipelineTest {
   def testHelloWorld {
     val spec = new PipelineTestSpec
     spec.name = "HelloWorld"
-    spec.args = "-S scala/qscript/examples/HelloWorld.scala"
+    spec.args = "-S public/scala/qscript/examples/HelloWorld.scala"
     PipelineTest.executeTest(spec)
   }
 
@@ -40,7 +40,7 @@ class HelloWorldPipelineTest {
   def testHelloWorldWithPrefix {
     val spec = new PipelineTestSpec
     spec.name = "HelloWorldWithPrefix"
-    spec.args = "-S scala/qscript/examples/HelloWorld.scala -jobPrefix HelloWorld"
+    spec.args = "-S public/scala/qscript/examples/HelloWorld.scala -jobPrefix HelloWorld"
     PipelineTest.executeTest(spec)
   }
 
@@ -48,7 +48,7 @@ class HelloWorldPipelineTest {
   def testHelloWorldWithPriority {
     val spec = new PipelineTestSpec
     spec.name = "HelloWorldWithPriority"
-    spec.args = "-S scala/qscript/examples/HelloWorld.scala -jobPriority 100"
+    spec.args = "-S public/scala/qscript/examples/HelloWorld.scala -jobPriority 100"
     PipelineTest.executeTest(spec)
   }
 }