deepvariant-build-test.md

Building DeepVariant from sources

DeepVariant comes with scripts to build it on Ubuntu 20.04. 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.

First install the Google Cloud SDK, because we will need to use its gsutil command to fetch some dependencies.

The build-prereq.sh command below will install a number of system packages to fulfill DeepVariant's prerequisites (using apt-get and pip, invoked via sudo). This commands also downloads and builds TensorFlow and CLIF from source.

First run sudo su, and then run the following commands to install prerequisites, build the DeepVariant programs, and then run tests.

./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.

If you want to rebuild the binaries on the same machine, here are the steps you can follow: #756 (comment)

Preparing a machine to run DeepVariant

The following command should be run on any machine on which you wish run DeepVariant, since there are runtime dependencies, such as Python packages like numpy and Tensorflow to be installed:

./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.