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Bump htsjdk/picard versions #376

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Merged
bbimber merged 2 commits into from
Jul 31, 2025
Merged

Bump htsjdk/picard versions #376

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88bc810
Make FastqcRunner more tolerant to HTSJDK version bumps
bbimber Jul 30, 2025
9bef6ce
Update HTSJDK and picard versions
bbimber Jul 29, 2025
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2 changes: 1 addition & 1 deletion SequenceAnalysis/build.gradle
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Original file line number Diff line number Diff line change
Expand Up @@ -123,7 +123,7 @@ dependencies {
BuildUtils.addExternalDependency(
project,
new ExternalDependency(
"com.github.broadinstitute:picard:3.1.0",
"com.github.broadinstitute:picard:3.4.0",
"Picard Tools Lib",
"PicardTools",
"https://github.com/broadinstitute/picard",
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23 changes: 22 additions & 1 deletion SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FastqcRunner.java
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Original file line number Diff line number Diff line change
Expand Up @@ -368,7 +368,7 @@ private List<String> getBaseParams() throws FileNotFoundException
throw new RuntimeException("Not found: " + jbzip2.getPath());
}

File htsjdkJar = new File(libDir, "htsjdk-4.0.0.jar");
File htsjdkJar = findJar(libDir, "htsjdk-");
if (!htsjdkJar.exists())
{
throw new RuntimeException("Not found: " + htsjdkJar.getPath());
Expand Down Expand Up @@ -403,6 +403,27 @@ private List<String> getBaseParams() throws FileNotFoundException
return params;
}

private File findJar(final File libDir, final String prefix)
{
if (!libDir.exists())
{
throw new RuntimeException("Missing directory: " + libDir);
}

List<String> jarNames = Arrays.stream(libDir.list()).filter(fn -> fn.startsWith(prefix)).sorted().toList();
if (jarNames.isEmpty())
{
throw new RuntimeException("Unable to find JAR with prefix: " + prefix);
}

if (jarNames.size() > 1)
{
_logger.info("More than one JAR found with prefix: " + prefix);
}

return new File(libDir, jarNames.get(jarNames.size() - 1));
}

private int getThreads()
{
return _threads;
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