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Picard's CollectMultipleMetrics in Queue v3.4 and v3.5
Some of the picard's collect (e.g.
CollectInsertSizeMetrics) commands load R script resources. Those resources were present in Queue <= v3.3-0 but they are absent from the subsequent versions.
$ jar tf 3.3-0/Queue.jar | grep "picard.*R$" picard/analysis/baseDistributionByCycle.R picard/analysis/gcBias.R picard/analysis/meanQualityByCycle.R picard/analysis/rnaSeqCoverage.R picard/analysis/qualityScoreDistribution.R picard/analysis/insertSizeHistogram.R $ jar tf 3.4-0/Queue.jar | grep "picard.*R$" $ jar tf 3.5-0/Queue.jar | grep "picard.*R$" $
Without those resources,
CollectMultipleMetrics throws something similar to
java.lang.IllegalArgumentException: Script [picard/analysis/qualityScoreDistribution.R] not found in classpath depending on which commands it hits first. I thought I would be able to overcome that by adding
CLASSPATH but it did not help. I had to add them to
Queue.jar in order to make it work.
It would be nice to have those resources back in the distributed