Add gradle task to ensure consistent location for commons-math

Author: bbimber

SequenceAnalysis/build.gradle

@@ -67,3 +67,21 @@ if (project.findProject(BuildUtils.getTestProjectPath(project.gradle)) != null &
       dependsOn(createPipelineConfigTask)
    }
 }
+
+project.task("copyJars",
+        type: Copy,
+        group: "Build",
+        description: "Copy JARs to external directory",
+        { CopySpec copy ->
+           copy.setDuplicatesStrategy(DuplicatesStrategy.EXCLUDE)
+           copy.from(project.configurations.external)
+           copy.into new File("${project.labkey.explodedModuleLibDir}")
+           copy.include {
+              "**commons-math3-**.jar"
+           }
+        }
+).doFirst({
+   
+})
+
+project.tasks.processModuleResources.dependsOn(project.tasks.copyJars)

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FastqcRunner.java

@@ -353,11 +353,6 @@ private List<String> getBaseParams() throws FileNotFoundException
         }
 
         File libDir = new File(ModuleLoader.getInstance().getModule(SequenceAnalysisModule.NAME).getExplodedPath(), "lib");
-        File coreLibDir = new File(ModuleLoader.getInstance().getModule("core").getExplodedPath(), "lib");
-        if (!coreLibDir.exists())
-        {
-            throw new RuntimeException("Not found: " + coreLibDir.getPath());
-        }
 
         File fastqcDir = new File(libDir.getParentFile(), "external/fastqc");
         File bzJar = new File(libDir, "bzip2-0.9.1.jar");
@@ -368,12 +363,10 @@ private List<String> getBaseParams() throws FileNotFoundException
         if (!samJar.exists())
             throw new RuntimeException("Not found: " + samJar.getPath());
 
-        File commonsMath = new File(coreLibDir, "commons-math3-3.6.1.jar");
+        File commonsMath = new File(libDir, "commons-math3-3.6.1.jar");
         if (!commonsMath.exists())
         {
-            File[] files = coreLibDir.listFiles();
-            String contents = files == null ? "null" : Arrays.stream(files).map(File::getName).filter(x -> x.contains("jar")).collect(Collectors.joining(","));
-            throw new RuntimeException("Not found: " + commonsMath.getPath() + ", files present: " + contents);
+            throw new RuntimeException("Not found: " + commonsMath.getPath());
         }
 
         List<String> classPath = new ArrayList<>();