Installing the GA4GH Schemas

The schemas are documents (text files) that formally describe the messages that pass between GA4GH servers and clients, which we also refer to collectively as “the API.” The schemas are written in a language called Protocol Buffers 3.

For instructions on how to install Protocol Buffers 3 on your system, consult the protocol buffers C++ installation instructions page.

We use the schemas in a couple of different ways:

  • to generate source code
  • to generate documentation

Generating Source Code

$ cd src/main/proto && protoc --python_out=. ga4gh/*

Installing the Documentation Tools and Generating Documentation

We use a tool called Sphinx to generate the documentation from Protocol Buffers input files.

Install prerequisites

To use the Sphinx/Protocol Buffers documentation generator, you must install some software packages it requires.

Maven

We use the Maven build tool to control processing the schemas. Installing Maven will also install Java.

Ubuntu
$ sudo apt-get install maven
CentOS/Fedora
$ sudo yum install maven
Mac OS X
$ brew install maven

Python/PIP

We use some Python utility programs also.

Install the Python installer pip.

Ubuntu
$ sudo apt-get install python-pip
CentOS/Fedora
$ sudo yum install python-pip
Mac OS X

Use brew:

$ brew install pip

Or download pip from here and run it:

$ python get-pip.py

Putting it all together

Do this once to install all required Python packages:

$ sudo pip install -r python/dev_requirements.txt -c python/constraints.txt

Generate the documentation

With those prerequisites out of the way, do this anytime you wish to generate the documentation.

Assuming your working directory is the base “schemas” directory, do this:

$ mvn site

The documentation you generate will reside in target/generated-docs/merged/html. To view it, open the file target/generated-docs/merged/html/index.html in a browser.