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MonashBioinformaticsPlatform / RNAsik-pipe

RNAsik - more than just a pipeline
https://monashbioinformaticsplatform.github.io/RNAsik-pipe/
Apache License 2.0
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Set default memory for picard SortSam, MarkDuplicates. #5

Closed pansapiens closed 6 years ago

pansapiens commented 7 years ago

This patch sets the default memory for the picard "prePro" steps to 16 Gb. This is required when BigDataScipt runs on an HPC cluster (eg SLURM) where RAM usage is enforced. This value can be configured in sik.config if required. 16 Gb is a conservative 'high' value that should prevent jobs being killed for typical runs.

serine commented 6 years ago

@pansapiens As you probably already know, this has got fixed recently, this is initial commit 8c0be8e48a9dc5b943f6b6b0fb2e867de180b6b8 . Note that there has been a few bug fixes so grab latest from master branch.

Thanks for PR, going to close this now