From 55cc6f4b5bb1ffec8f39babad99b27e472c46c6c Mon Sep 17 00:00:00 2001 From: bbimber Date: Fri, 29 Nov 2024 15:33:22 -0800 Subject: [PATCH] Attempt to remove copyJars() from SequenceAnalysis gradle build --- SequenceAnalysis/build.gradle | 18 +----------------- .../run/util/FastqcRunner.java | 10 ++-------- 2 files changed, 3 insertions(+), 25 deletions(-) diff --git a/SequenceAnalysis/build.gradle b/SequenceAnalysis/build.gradle index f085ebe5c..ead7f308a 100644 --- a/SequenceAnalysis/build.gradle +++ b/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) } +} \ No newline at end of file diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FastqcRunner.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FastqcRunner.java index f30999c92..8252c7876 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FastqcRunner.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FastqcRunner.java @@ -374,7 +374,8 @@ private List 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 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 classPath = new ArrayList<>(); classPath.add("."); classPath.add(fastqcDir.getPath());