Explicitly set `_JAVA_OPTIONS` before calling Picard

kundajelab / chipseq_pipeline

AQUAS TF and histone ChIP-seq pipeline

BSD 3-Clause "New" or "Revised" License

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Explicitly set `_JAVA_OPTIONS` before calling Picard #3

Closed chrisprobert closed 8 years ago

chrisprobert commented 8 years ago

If a user has _JAVA_OPTIONS set, at runtime JVM will ignore our -Xmx4G flag and use the user's setting. Due to unpredictable picard heap space, this was causing unreproducible crashes for me. To fix, we can explicitly set _JAVA_OPTIONS before calling Picard, just like we do in atac.bds: https://github.com/kundajelab/bds_atac/blob/master/atac.bds#L814