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  • Since there is still no information about backends in the User Guide I'll give an answer to my own question. The only comprehensive source of information is the readme file on the github https://github.com/broadinstitute/cromwell but unfortunately …
  • Thank you, yes I saw that pull request which went into 0.19 hotfix and which confused me a lot because I could not find the traces of it in the current development branch.
  • Unfortunately there are still issues installing Oncotator. The principal issue related to v 1.8.0.0 is that it requires pysam 0.7.5 which is not available from pypi. As a result oncotator setup gives an error about missing pysam. The dependencies sc…
  • Having spent a few days making Oncotator to work, I want to share my solution. I think the main problem stems from the fact that Oncotator uses distribute-0.6.15 which does not understand wheel format (new Python packaging). Therefore if you happen …
  • Hello, everyone! Just want to add another voice for the need of an LSF patch. We are running LSF 9.1. Thanks
  • Thank you both. Yes, I am asking about handling of edge of intervals. I've seen the article but not sure how it relates to the default scatter/gather performed by GATK/Queue.