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wtsi-hgi / gatk-cwl-generator

Generates CWL files from the GATK documentation
MIT License
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java being run with -D64 instead of -d64 #18

Open ThomasHickman opened 6 years ago

ThomasHickman commented 6 years ago

From https://github.com/wtsi-hgi/arvados-pipelines/issues/7:

https://github.com/wtsi-hgi/arvados-pipelines/blob/master/cwl/tools/gatk-4.0/HaplotypeCaller.cwl#L5

-d64 is an option that tells Java to make sure to use 64 bit mode (although almost certainly it is the default anyway). -D64 might not mean anything, or perhaps it sets a system property named 64 to no value? It is not clear, but it is not the same as -d64:

$ docker run -it mercury/gatk-4.0.0.0:v1 java -h | grep '\-d64'
    -d64          use a 64-bit data model if available
$ docker run -it mercury/gatk-4.0.0.0:v1 java -h | grep -A 1 '\-D'
    -D<name>=<value>
                  set a system property
sersorrel commented 6 years ago

I can't see either -d64 or -D64 in any CWL files I've generated, nor can I find any commits that include either of those strings in this repo - is this definitely an issue with gatk-cwl-generator? (maybe --gatk_command was set to include -D64 when the CWL files in question were generated?)