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Added documentation on OMP_NUM_THREADS and MKL_NUM_THREADS to Germlin…
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…eCNVCaller and DetermineGermlineContigPloidy. (#8223)
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samuelklee authored Mar 16, 2023
1 parent bab0adc commit 2dbc025
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* the python environment is already set up. Otherwise, the environment must be created and activated as described in the
* main GATK README.md file.</p>
*
* <p>OpenMP and MKL parallelism can be controlled by setting the <code>OMP_NUM_THREADS</code> and <code>MKL_NUM_THREADS</code>
* environment variables, respectively.</p>
*
* <p>Advanced users may wish to set the <code>THEANO_FLAGS</code> environment variable to override the GATK theano
* configuration. For example, by running
* <code>THEANO_FLAGS="base_compiledir=PATH/TO/BASE_COMPILEDIR" gatk DetermineGermlineContigPloidy ...</code>, users can specify
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* the python environment is already set up. Otherwise, the environment must be created and activated as described in the
* main GATK README.md file.</p>
*
* <p>OpenMP and MKL parallelism can be controlled by setting the <code>OMP_NUM_THREADS</code> and <code>MKL_NUM_THREADS</code>
* environment variables, respectively.</p>
*
* <p>Advanced users may wish to set the <code>THEANO_FLAGS</code> environment variable to override the GATK theano
* configuration. For example, by running
* <code>THEANO_FLAGS="base_compiledir=PATH/TO/BASE_COMPILEDIR" gatk GermlineCNVCaller ...</code>, users can specify
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