In order to install BioNetDB, the following packages are required:
Java 1.8.0_60+
Neo4j graph database
Apache Maven (when building BioNetDB from sources)
Installing Neo4j
In order to install Neo4j, follow the instructions from the Neo4j Operation Manual powered by the Neo4j Team. This describes how to install Neo4j in different deployment contexts, such as Linux, Mac OS, Windows, Debian, Docker.
Installing BioNetDB
You can install BioNetDB from the binaries or from the source code. Next sections describe both methods in details.
Extract the contents of the archive using tar -xfz <filename> for the .tar.gz file, or gunzip <filename> for the .zip file.
Run the BioNetDB command line: build/bin/bionetdb.sh
Building from source code
Prerequisites
In order to build BioNetDB from source code you must first get the source code of BioNetDB from GitHub, most of the dependencies - including OpenCB dependencies - will be fetched from Maven Central Repository, however in some scenarios OpenCB dependencies will need to be built from GitHub source code. Compiling and building processes are carried out by Apache Maven. The following tools are required for successful build:
