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Attempt to remove copyJars() from SequenceAnalysis gradle build #306

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Merged
bbimber merged 1 commit into from
Nov 30, 2024
Merged

Attempt to remove copyJars() from SequenceAnalysis gradle build #306

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18 changes: 1 addition & 17 deletions SequenceAnalysis/build.gradle
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Original file line number Diff line number Diff line change
Expand Up @@ -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) }
}
10 changes: 2 additions & 8 deletions SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FastqcRunner.java
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Expand Up @@ -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());
Expand All @@ -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());
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