diff --git a/src/main/java/org/broadinstitute/hellbender/tools/copynumber/DetermineGermlineContigPloidy.java b/src/main/java/org/broadinstitute/hellbender/tools/copynumber/DetermineGermlineContigPloidy.java index c29d1067ef8..fe07f4619be 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/copynumber/DetermineGermlineContigPloidy.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/copynumber/DetermineGermlineContigPloidy.java @@ -58,6 +58,14 @@ * the python environment is already set up. Otherwise, the environment must be created and activated as described in the * main GATK README.md file.

* + *

Advanced users may wish to set the THEANO_FLAGS environment variable to override the GATK theano + * configuration. For example, by running + * THEANO_FLAGS="base_compiledir=PATH/TO/BASE_COMPILEDIR" gatk DetermineGermlineContigPloidy ..., users can specify + * the theano compilation directory (which is set to $HOME/.theano by default). See theano documentation + * at + * http://deeplearning.net/software/theano/library/config.html. + *

+ * *

Tool run modes

* *

This tool has two operation modes as described below:

diff --git a/src/main/java/org/broadinstitute/hellbender/tools/copynumber/GermlineCNVCaller.java b/src/main/java/org/broadinstitute/hellbender/tools/copynumber/GermlineCNVCaller.java index 8875ee448b1..99dfa000c72 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/copynumber/GermlineCNVCaller.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/copynumber/GermlineCNVCaller.java @@ -70,6 +70,14 @@ * the python environment is already set up. Otherwise, the environment must be created and activated as described in the * main GATK README.md file.

* + *

Advanced users may wish to set the THEANO_FLAGS environment variable to override the GATK theano + * configuration. For example, by running + * THEANO_FLAGS="base_compiledir=PATH/TO/BASE_COMPILEDIR" gatk GermlineCNVCaller ..., users can specify + * the theano compilation directory (which is set to $HOME/.theano by default). See theano documentation + * at + * http://deeplearning.net/software/theano/library/config.html. + *

+ * *

Tool run modes

*
*
COHORT mode:
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/copynumber/PostprocessGermlineCNVCalls.java b/src/main/java/org/broadinstitute/hellbender/tools/copynumber/PostprocessGermlineCNVCalls.java index e7051457866..73eb2200351 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/copynumber/PostprocessGermlineCNVCalls.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/copynumber/PostprocessGermlineCNVCalls.java @@ -61,7 +61,24 @@ * calls of {@link DetermineGermlineContigPloidy}.

* *

Finally, the tool concatenates posterior means for denoised copy ratios from all the call shards produced by - * the {@link GermlineCNVCaller} into a single file.

+ * the {@link GermlineCNVCaller} into a single file.

+ * + *

Python environment setup

+ * + *

The computation done by this tool, aside from input data parsing and validation, is performed outside of the Java + * Virtual Machine and using the gCNV computational python module, namely {@code gcnvkernel}. It is crucial that + * the user has properly set up a python conda environment with {@code gcnvkernel} and its dependencies + * installed. If the user intends to run {@link PostprocessGermlineCNVCalls} using one of the official GATK Docker images, + * the python environment is already set up. Otherwise, the environment must be created and activated as described in the + * main GATK README.md file.

+ * + *

Advanced users may wish to set the THEANO_FLAGS environment variable to override the GATK theano + * configuration. For example, by running + * THEANO_FLAGS="base_compiledir=PATH/TO/BASE_COMPILEDIR" gatk PostprocessGermlineCNVCalls ..., users can specify + * the theano compilation directory (which is set to $HOME/.theano by default). See theano documentation + * at + * http://deeplearning.net/software/theano/library/config.html. + *

* *

Required inputs:

*