Attempt to remove copyJars() from SequenceAnalysis gradle build

Author: bbimber

SequenceAnalysis/build.gradle

@@ -200,20 +200,4 @@ if (project.findProject(BuildUtils.getTestProjectPath(project.gradle)) != null &
             }
         }
     }
-}
-
-project.tasks.register("copyJars", Copy)
-        { CopySpec copy ->
-            copy.group = "Build"
-            copy.description = "Copy commons-math3 JAR to module's lib directory"
-
-            copy.setDuplicatesStrategy(DuplicatesStrategy.EXCLUDE)
-            copy.from(project.configurations.external)
-            copy.into new File("${project.labkey.explodedModuleLibDir}")
-            copy.include {
-                "**commons-math3-**.jar"
-            }
-        }
-
-project.tasks.named('module').configure { dependsOn(project.tasks.copyJars) }
-project.tasks.named('copyJars').configure { mustRunAfter(project.tasks.populateExplodedLib) }
+}

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

@@ -374,7 +374,8 @@ private List<String> getBaseParams() throws FileNotFoundException
             throw new RuntimeException("Not found: " + htsjdkJar.getPath());
         }
 
-        File commonsMath = new File(libDir, "commons-math3-3.6.1.jar");
+        File apiLibDir = new File(ModuleLoader.getInstance().getModule("api").getExplodedPath(), "lib");
+        File commonsMath = new File(apiLibDir, "commons-math3-3.6.1.jar");
         if (!commonsMath.exists())
         {
             throw new RuntimeException("Not found: " + commonsMath.getPath());
@@ -386,13 +387,6 @@ private List<String> getBaseParams() throws FileNotFoundException
             throw new RuntimeException("Not found: " + jhdf5.getPath());
         }
 
-        // NOTE: FastQC expects an alternate package name within this JAR, so use their packaged code instead:
-//        File base64 = new File(libDir, "base64-2.3.8.jar");
-//        if (!base64.exists())
-//        {
-//            throw new RuntimeException("Not found: " + base64.getPath());
-//        }
-
         List<String> classPath = new ArrayList<>();
         classPath.add(".");
         classPath.add(fastqcDir.getPath());