diff --git a/SequenceAnalysis/build.gradle b/SequenceAnalysis/build.gradle
index ec2b23476..f085ebe5c 100644
--- a/SequenceAnalysis/build.gradle
+++ b/SequenceAnalysis/build.gradle
@@ -163,7 +163,7 @@ dependencies {
 if (project.findProject(BuildUtils.getTestProjectPath(project.gradle)) != null && project.hasProperty("teamcity"))
 {
     project.evaluationDependsOn(BuildUtils.getTestProjectPath(project.gradle))
-    def configDir = "${ServerDeployExtension.getServerDeployDirectory(project)}/config"
+    def configDir = new File(ServerDeployExtension.getServerDeployDirectory(project), "config")
     def testProject = project.findProject(BuildUtils.getTestProjectPath(project.gradle))
     def createPipelineConfigTask = project.tasks.register("createPipelineConfig", Copy) {
         Copy task ->
@@ -183,13 +183,9 @@ if (project.findProject(BuildUtils.getTestProjectPath(project.gradle)) != null &
                 return newLine
 
             })
-            task.destinationDir = new File(configDir)
+            task.destinationDir = configDir
 
             if (BuildUtils.useEmbeddedTomcat(project)) {
-                task.doFirst {
-                    new File(new File(BuildUtils.getEmbeddedConfigPath(project)), "application.properties") << "\n${configDir}"
-                }
-
                 rootProject.allprojects {
                     task.mustRunAfter tasks.withType(DoThenSetup)
                 }
@@ -199,7 +195,8 @@ if (project.findProject(BuildUtils.getTestProjectPath(project.gradle)) != null &
         dependsOn(createPipelineConfigTask)
         if (BuildUtils.useEmbeddedTomcat(project)) {
             it.doFirst {
-                new File(new File(BuildUtils.getEmbeddedConfigPath(project)), "application.properties") << "\ncontext.pipelineConfig=${configDir}"
+                new File(new File(BuildUtils.getEmbeddedConfigPath(project)), "application.properties")
+                        << "\ncontext.pipelineConfig=${configDir.getAbsolutePath().replace("\\", "\\\\")}"
             }
         }
     }
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceRemoteIntegrationTests.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceRemoteIntegrationTests.java
index faa074c82..3a1ecf590 100644
--- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceRemoteIntegrationTests.java
+++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceRemoteIntegrationTests.java
@@ -83,10 +83,12 @@ private File setupConfigDir(File outDir) throws IOException
 
                     path = path.replaceAll("\\\\", "/");
                     line = line.replaceAll("@@SEQUENCEANALYSIS_TOOLS@@", path);
+                    _log.info("Writing to pipelineConfig.xml: " + line);
                 }
                 else if (line.contains("@@WORK_DIR@@"))
                 {
                     line = line.replaceAll("@@WORK_DIR@@", outDir.getPath().replaceAll("\\\\", "/"));
+                    _log.info("Writing to pipelineConfig.xml: " + line);
                 }
 
                 writer.println(line);
@@ -213,6 +215,8 @@ protected void executeJobRemote(File workDir, @Nullable File jobJson) throws IOE
         ProcessBuilder pb = new ProcessBuilder(args);
         pb.directory(workDir);
 
+        _log.info("Executing job in '" + pb.directory().getAbsolutePath() + "': " + String.join(" ", pb.command()));
+
         Process proc;
         try
         {