Goby is an open source next-gen data management framework and is distributed under the GNU General Public License (GPL). Goby package is available as precompiled files and also in source code form. Distribution types are described in the following sections.
The binary distribution is intended for end users who wish to align and/or analyze for datasets they are interested in. The binary distribution of the Goby package is comprised of a single file as described as follows:
- This includes all the external classes and sample data needed to run Goby
In order to make use of the Goby package, the following packages are also required.
The binary distribution of Goby is a single zip file. It can be extracted to a directory of your choosing. Throughout the documentation, this location will be referred to as the "<install-dir>"
A Java virtual machine is required for Goby. The JDK should not be required for the binary distribution. The examples assume the java executable is on the system path.
The source distribution of the Goby package contains the Java source code along with supporting files that are used to compile and test the package. See the Goby page to download the latest release of the source code.
This project's Subversion repository can be checked out through SVN with the following instruction set:
Additionally you can browse the Goby project source code in the Subversion repository.
NOTE: Use username "guest" and your email address at the login prompt if you do not have an account with the ICB.
In addition to the packages in the Binary Distribution the following Java packages are required in order to build and use Goby.
- Java Development Kit (JDK) 1.6+
- BDVAL API
- Fastutil Fast and compact type-specific collections for Java
- JSAP Java-based Simple Argument Parser
- DSI Utilities
- Commons Collections
- Commons Configuration
- Commons Exec
- Commons Lang
- Commons Logging
- Commons Math
- Commons I/O
- Colt Open Source Libraries for High Performance Scientific and Technical Computing in Java
- Crover CLI
- Google protobuf Google's data interchange format