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deepvariant-build-test.md

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Building DeepVariant from sources

DeepVariant comes with scripts to build it on Ubuntu 14 and 16, with Ubuntu 16 recommended. It can likely be built and run on other unix-based systems with some minimal modifications to these scripts. One way to get access to a machine running Ubuntu is through a cloud computing platform like Google Cloud Engine; see for example the instructions at the beginning of the DeepVariant Quick Start.

To build and test DeepVariant, run the following commands:

./build-prereq.sh

./build_and_test.sh

At the end of the output of that last command, you should see a summary message like "Executed 55 out of 55 tests: 55 tests pass." along with the message "Target //deepvariant:binaries up-to-date:" followed by a list of the just-built deepvariant binaries.

Preparing a machine to run DeepVariant

The following command should be run on any machine on which you wish run DeepVariant:

./run-prereq.sh

Configuring the build

Advanced users may want to edit the settings.sh file before building. It contains options for configuring TensorFlow, CUDA, GPU usage, etc.