diff --git a/build.gradle b/build.gradle
index fc5eb041e0..ec5f085f53 100644
--- a/build.gradle
+++ b/build.gradle
@@ -125,32 +125,23 @@ if (!BuildUtils.isIntellij())  {
     }
 }
 
-def initPropertiesTask = project.tasks.register("initProperties", Task) {
-    Task task ->
+def initPropertiesTask = project.tasks.register("initProperties", Copy) {
+    Copy task ->
         task.group = GroupNames.TEST
         task.description = "Create test.properties if missing"
-        task.doLast({
-            File testProperties = project.file('test.properties')
-            File testPropertiesTemplate = project.file('test.properties.template')
-
-            if (!testProperties.exists())
-            {
-                project.copy {
-                    CopySpec copy ->
-                        copy.from(testPropertiesTemplate)
-                        copy.into(project.file("."))
-                        copy.rename(testPropertiesTemplate.getName(), testProperties.getName())
-                        copy.filter { String line ->
-                            if (line.startsWith("#!!")) {
-                                return null
-                            }
-                            else {
-                                return line
-                            }
-                        }
-                }
+        task.from(project.file('test.properties.template'))
+        task.into(".")
+        task.outputs.files(project.file('test.properties'))
+        task.rename('test.properties.template', 'test.properties')
+        task.filter { String line ->
+            if (line.startsWith("#!!")) {
+                return null
             }
-        })
+            else {
+                return line
+            }
+        }
+        task.onlyIf{ !project.file('test.properties').exists() }
 }
 
 project.tasks.register("convertHarToStressXml", JavaExec) {
diff --git a/data/qc/build.gradle b/data/qc/build.gradle
index 38757cafeb..c4d1e9b930 100644
--- a/data/qc/build.gradle
+++ b/data/qc/build.gradle
@@ -16,6 +16,10 @@ sourceSets {
   }
 }
 
+// We declare that these jar file tasks must run after the sample data file task since writeSampleDataFile declares the
+// testAutomation/data directory as an input.
+def sampleDataFileTask = project.project(BuildUtils.getTestProjectPath(project.gradle)).tasks.named("writeSampleDataFile")
+
 project.tasks.register('validatorJar', Jar) {
     group = "QC"
     description = "Builds jar for assay validation"
@@ -31,6 +35,7 @@ project.tasks.register('validatorJar', Jar) {
                 'Built-By': System.getProperty("user.name"),
                 'Main-Class': 'org.labkey.AssayValidator'
     }
+    sampleDataFileTask.get().mustRunAfter(it)
 }
 
 project.tasks.register('transformJar', Jar) {
@@ -48,6 +53,7 @@ project.tasks.register('transformJar', Jar) {
                 'Built-By': System.getProperty("user.name"),
                 'Main-Class': 'org.labkey.AssayTransform'
     }
+    sampleDataFileTask.get().mustRunAfter(it)
 }
 
 project.tasks.register('transformNoopJar', Jar) {
@@ -65,6 +71,7 @@ project.tasks.register('transformNoopJar', Jar) {
                 'Built-By': System.getProperty("user.name"),
                 'Main-Class': 'org.labkey.AssayTransformNoOp'
     }
+    sampleDataFileTask.get().mustRunAfter(it)
 }
 
 project.tasks.register('transformWarningJar', Jar) {
@@ -82,6 +89,7 @@ project.tasks.register('transformWarningJar', Jar) {
                 'Built-By': System.getProperty("user.name"),
                 'Main-Class': 'org.labkey.AssayTransformWarning'
     }
+    sampleDataFileTask.get().mustRunAfter(it)
 }
 
 var jarTask = project.tasks.named('jar')
diff --git a/distributions/teamcity/build.gradle b/distributions/teamcity/build.gradle
index 128edeb44c..f499b8e7ef 100644
--- a/distributions/teamcity/build.gradle
+++ b/distributions/teamcity/build.gradle
@@ -12,7 +12,7 @@ plugins {
 if (!BuildUtils.isOpenSource(project))
     apply plugin: 'org.labkey.build.applyLicenses'
 
-dist.description = "Distribution that includes all modules, for use in the continuous integration LabKey Server instance"
+description = "Distribution that includes all modules, for use in the continuous integration LabKey Server instance"
 
 project.tasks.register("distribution", ModuleDistribution) {
     ModuleDistribution dist ->
diff --git a/src/org/labkey/test/TestFileUtils.java b/src/org/labkey/test/TestFileUtils.java
index 3af44b7639..c983d5237b 100644
--- a/src/org/labkey/test/TestFileUtils.java
+++ b/src/org/labkey/test/TestFileUtils.java
@@ -226,11 +226,11 @@ public static File getModulesDir()
     {
         if (_modulesDir == null)
         {
-            _modulesDir = new File(getDefaultDeployDir(), "modules");
+            // Module root when deploying from embedded distribution
+            _modulesDir =  new File(getDefaultDeployDir(), "embedded/modules");
             if (!_modulesDir.isDirectory())
             {
-                // Module root when deploying from embedded distribution
-                _modulesDir = new File(getDefaultDeployDir(), "embedded/modules");
+                _modulesDir = new File(getDefaultDeployDir(), "modules");
             }
         }
         return _modulesDir;