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Added ability to override THEANO_FLAGS environment variable in gCNV tools. #6244

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merged 1 commit into from
Nov 7, 2019

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samuelklee
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@samuelklee samuelklee commented Nov 4, 2019

Closes #6235

This PR allows users to more easily clobber individual theano flags. This can be used to change the location of the theano compilation directory (see the above issue and #4782 for context). These flags are set upon import of the theano module; see http://deeplearning.net/software/theano/library/config.html for details.

This solution is a little hacky, hence the code duplication. Ideally, we'd be able to specify this directory (and potentially other flags) as a parameter to the tools. As discussed with @cmnbroad, probably the cleanest solution would be to modify the PythonScriptExecutor to allow environment variables to be specified, e.g. via ProcessSettings. This solution would also cover the initial import of the gcnvkernel package for validation purposes, rather than only the imports in the resource scripts modified in this PR.

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@mwalker174 this branch is probably ready for review. Thanks!

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Thanks this looks good!

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ramdom BUGS for germline copy number variants calling with GATK 4. PythonScriptExecutorException
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